HEADER OXIDOREDUCTASE(CHOH (D)-NAD(P)+ (A)) 22-SEP-93 1GDH 1GDH 2 COMPND D-GLYCERATE DEHYDROGENASE (APO FORM) (E.C.1.1.1.29) 1GDH 3 SOURCE (HYPHOMICROBIUM METHYLOVORUM) 1GDH 4 AUTHOR J.D.GOLDBERG,T.YOSHIDA,P.BRICK 1GDH 5 REVDAT 2 20-JUL-95 1GDHA 1 JRNL REMARK 1GDHA 1 REVDAT 1 31-JAN-94 1GDH 0 1GDH 6 JRNL AUTH J.D.GOLDBERG,T.YOSHIDA,P.BRICK 1GDH 7 JRNL TITL CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE 1GDH 8 JRNL TITL 2 DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION 1GDH 9 JRNL REF J.MOL.BIOL. V. 236 1123 1994 1GDHA 2 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 0070 1GDHA 3 REMARK 1 1GDH 12 REMARK 1 REFERENCE 1 1GDH 13 REMARK 1 AUTH J.D.GOLDBERG,P.BRICK,T.YOSHIDA,T.MITSUNAGA, 1GDH 14 REMARK 1 AUTH 2 T.OSHIRO,M.SHIMAO,Y.IZUMI 1GDH 15 REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY DIFFRACTION 1GDH 16 REMARK 1 TITL 2 STUDIES OF HYDROXYPYRUVATE REDUCTASE (D-GLYCERATE 1GDH 17 REMARK 1 TITL 3 DEHYDROGENASE) FROM HYPHOMICROBIUM METHYLOVORUM 1GDH 18 REMARK 1 REF J.MOL.BIOL. V. 225 909 1992 1GDH 19 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 0070 1GDHA 4 REMARK 2 1GDH 21 REMARK 2 RESOLUTION. 2.4 ANGSTROMS. 1GDH 22 REMARK 3 1GDH 23 REMARK 3 REFINEMENT. 1GDH 24 REMARK 3 PROGRAM X-PLOR 1GDH 25 REMARK 3 AUTHORS BRUNGER 1GDH 26 REMARK 3 R VALUE 0.189 1GDH 27 REMARK 3 RMSD BOND DISTANCES 0.010 ANGSTROMS 1GDH 28 REMARK 3 RMSD BOND ANGLES 1.48 DEGREES 1GDH 29 REMARK 4 1GDH 30 REMARK 4 THE MOLECULE IS A DIMER AND TWO SUBUNITS ARE CONTAINED IN 1GDH 31 REMARK 4 THE CRYSTALLOGRAPHIC TRICLINIC UNIT CELL RELATED BY AN 1GDH 32 REMARK 4 APPROXIMATE TWO-FOLD AXIS. THESE SUBUNITS HAVE BEEN 1GDH 33 REMARK 4 ASSIGNED CHAIN IDENTIFIERS *A* AND *B* IN THIS ENTRY. THE 1GDH 34 REMARK 4 TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL 1GDH 35 REMARK 4 YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED 1GDH 36 REMARK 4 TO CHAIN *B*. 1GDH 37 REMARK 5 1GDH 38 REMARK 5 THE WATER MOLECULES ARE NUMBERED FROM 400A AND 400B 1GDH 39 REMARK 5 ONWARDS, ACCORDING TO THE SUBUNIT TO WHICH THEY MOST 1GDH 40 REMARK 5 CLOSELY CORRESPOND. 1GDH 41 REMARK 6 1GDH 42 REMARK 6 ONLY PARTIAL DNA SEQUENCE INFORMATION IS AVAILABLE. 1GDH 43 REMARK 6 THE DNA SEQUENCE CORRESPONDING TO THE 130 N-TERMINAL 1GDH 44 REMARK 6 RESIDUES IS KNOWN. FOR THE REMAINDER OF THE POLYPEPTIDE, 1GDH 45 REMARK 6 SIDE-CHAIN IDENTITIES HAVE BEEN INTERPRETED DIRECTLY FROM 1GDH 46 REMARK 6 ELECTRON DENSITY MAPS. THE POSSIBILITY OF THERE BEING 1GDH 47 REMARK 6 ADDITIONAL RESIDUES AT THE C-TERMINUS IS NOT DISCOUNTED. 1GDH 48 REMARK 7 1GDH 49 REMARK 7 THE FOLLOWING RESIDUES HAVE NO SIGNIFICANT ELECTRON DENSITY 1GDH 50 REMARK 7 IN FINAL MAP AND HAVE CONSEQUENTLY BEEN OMITTED FROM THE 1GDH 51 REMARK 7 MODEL: 1A, 1B. 1GDH 52 REMARK 8 1GDH 53 REMARK 8 THE FOLLOWING RESIDUES CONTAIN SIDE CHAIN ATOMS WHICH HAVE 1GDH 54 REMARK 8 NO SIGNIFICANT ELECTRON DENSITY IN THE FINAL MAP AND HAVE 1GDH 55 REMARK 8 THEREFORE BEEN OMITTED FROM THE MODEL: LYS A 2, LYS A 3, 1GDH 56 REMARK 8 GLU A 41, LYS A 44, LYS A 56, ARG A 58, LYS A 59, GLU A 60, 1GDH 57 REMARK 8 ARG A 64, LYS A 70, LYS A 88, LYS B 2, LYS B 3, LYS B 4, 1GDH 58 REMARK 8 ASP B 31, LYS B 56, GLU B 59, ASN B 64, LYS B 88, LYS B 93, 1GDH 59 REMARK 8 GLU B 216, ARG B 218. 1GDH 60 REMARK 9 1GDHA 5 REMARK 9 CORRECTION. UPDATE JRNL REFERENCE TO REFLECT PUBLICATION. 1GDHA 6 REMARK 9 REVISE CODEN FOR REFERENCE 1. 20-JUL-95. 1GDHA 7 SEQRES 1 A 320 LYS LYS LYS ILE LEU ILE THR TRP PRO LEU PRO GLU ALA 1GDH 61 SEQRES 2 A 320 ALA MET ALA ARG ALA ARG GLU SER TYR ASP VAL ILE ALA 1GDH 62 SEQRES 3 A 320 HIS GLY ASP ASP PRO LYS ILE THR ILE ASP GLU MET ILE 1GDH 63 SEQRES 4 A 320 GLU THR ALA LYS SER VAL ASP ALA LEU LEU ILE THR LEU 1GDH 64 SEQRES 5 A 320 ASN GLU LYS CYS ARG LYS GLU VAL ILE ASP ARG ILE PRO 1GDH 65 SEQRES 6 A 320 GLU ASN ILE LYS CYS ILE SER THR TYR SER ILE GLY PHE 1GDH 66 SEQRES 7 A 320 ASP HIS ILE ASP LEU ASP ALA CYS LYS ALA ARG GLY ILE 1GDH 67 SEQRES 8 A 320 LYS VAL GLY ASN ALA PRO HIS GLY VAL THR VAL ALA THR 1GDH 68 SEQRES 9 A 320 ALA GLU ILE ALA MET LEU LEU LEU LEU GLY SER ALA ARG 1GDH 69 SEQRES 10 A 320 ARG ALA GLY GLU GLY GLU LYS MET ILE ARG THR ARG SER 1GDH 70 SEQRES 11 A 320 TRP PRO GLY TRP GLU PRO LEU GLU LEU VAL GLY GLU LYS 1GDH 71 SEQRES 12 A 320 LEU ASP ASN LYS THR LEU GLY ILE TYR GLY PHE GLY SER 1GDH 72 SEQRES 13 A 320 ILE GLY GLN ALA LEU ALA LYS ARG ALA GLN GLY PHE ASP 1GDH 73 SEQRES 14 A 320 MET ASP ILE ASP TYR PHE ASP THR HIS ARG ALA SER SER 1GDH 74 SEQRES 15 A 320 SER ASP GLU ALA SER TYR GLN ALA THR PHE HIS ASP SER 1GDH 75 SEQRES 16 A 320 LEU ASP SER LEU LEU SER VAL SER GLN PHE PHE SER LEU 1GDH 76 SEQRES 17 A 320 ASN ALA PRO SER THR PRO GLU THR ARG TYR PHE PHE ASN 1GDH 77 SEQRES 18 A 320 LYS ALA THR ILE LYS SER LEU PRO GLN GLY ALA ILE VAL 1GDH 78 SEQRES 19 A 320 VAL ASN THR ALA ARG GLY ASP LEU VAL ASP ASN GLU LEU 1GDH 79 SEQRES 20 A 320 VAL VAL ALA ALA LEU GLU ALA GLY ARG LEU ALA TYR ALA 1GDH 80 SEQRES 21 A 320 GLY PHE ASP VAL PHE ALA GLY GLU PRO ASN ILE ASN GLU 1GDH 81 SEQRES 22 A 320 GLY TYR TYR ASP LEU PRO ASN THR PHE LEU PHE PRO HIS 1GDH 82 SEQRES 23 A 320 ILE GLY SER ALA ALA THR GLN ALA ARG GLU ASP MET ALA 1GDH 83 SEQRES 24 A 320 HIS GLN ALA ASN ASP LEU ILE ASP ALA LEU PHE GLY GLY 1GDH 84 SEQRES 25 A 320 ALA ASP MET SER TYR ALA LEU ALA 1GDH 85 SEQRES 1 B 320 LYS LYS LYS ILE LEU ILE THR TRP PRO LEU PRO GLU ALA 1GDH 86 SEQRES 2 B 320 ALA MET ALA ARG ALA ARG GLU SER TYR ASP VAL ILE ALA 1GDH 87 SEQRES 3 B 320 HIS GLY ASP ASP PRO LYS ILE THR ILE ASP GLU MET ILE 1GDH 88 SEQRES 4 B 320 GLU THR ALA LYS SER VAL ASP ALA LEU LEU ILE THR LEU 1GDH 89 SEQRES 5 B 320 ASN GLU LYS CYS ARG LYS GLU VAL ILE ASP ARG ILE PRO 1GDH 90 SEQRES 6 B 320 GLU ASN ILE LYS CYS ILE SER THR TYR SER ILE GLY PHE 1GDH 91 SEQRES 7 B 320 ASP HIS ILE ASP LEU ASP ALA CYS LYS ALA ARG GLY ILE 1GDH 92 SEQRES 8 B 320 LYS VAL GLY ASN ALA PRO HIS GLY VAL THR VAL ALA THR 1GDH 93 SEQRES 9 B 320 ALA GLU ILE ALA MET LEU LEU LEU LEU GLY SER ALA ARG 1GDH 94 SEQRES 10 B 320 ARG ALA GLY GLU GLY GLU LYS MET ILE ARG THR ARG SER 1GDH 95 SEQRES 11 B 320 TRP PRO GLY TRP GLU PRO LEU GLU LEU VAL GLY GLU LYS 1GDH 96 SEQRES 12 B 320 LEU ASP ASN LYS THR LEU GLY ILE TYR GLY PHE GLY SER 1GDH 97 SEQRES 13 B 320 ILE GLY GLN ALA LEU ALA LYS ARG ALA GLN GLY PHE ASP 1GDH 98 SEQRES 14 B 320 MET ASP ILE ASP TYR PHE ASP THR HIS ARG ALA SER SER 1GDH 99 SEQRES 15 B 320 SER ASP GLU ALA SER TYR GLN ALA THR PHE HIS ASP SER 1GDH 100 SEQRES 16 B 320 LEU ASP SER LEU LEU SER VAL SER GLN PHE PHE SER LEU 1GDH 101 SEQRES 17 B 320 ASN ALA PRO SER THR PRO GLU THR ARG TYR PHE PHE ASN 1GDH 102 SEQRES 18 B 320 LYS ALA THR ILE LYS SER LEU PRO GLN GLY ALA ILE VAL 1GDH 103 SEQRES 19 B 320 VAL ASN THR ALA ARG GLY ASP LEU VAL ASP ASN GLU LEU 1GDH 104 SEQRES 20 B 320 VAL VAL ALA ALA LEU GLU ALA GLY ARG LEU ALA TYR ALA 1GDH 105 SEQRES 21 B 320 GLY PHE ASP VAL PHE ALA GLY GLU PRO ASN ILE ASN GLU 1GDH 106 SEQRES 22 B 320 GLY TYR TYR ASP LEU PRO ASN THR PHE LEU PHE PRO HIS 1GDH 107 SEQRES 23 B 320 ILE GLY SER ALA ALA THR GLN ALA ARG GLU ASP MET ALA 1GDH 108 SEQRES 24 B 320 HIS GLN ALA ASN ASP LEU ILE ASP ALA LEU PHE GLY GLY 1GDH 109 SEQRES 25 B 320 ALA ASP MET SER TYR ALA LEU ALA 1GDH 110 FTNOTE 1 1GDH 111 FTNOTE 1 CIS PROLINE - PRO A 270 1GDH 112 FTNOTE 2 1GDH 113 FTNOTE 2 CIS PROLINE - PRO B 270 1GDH 114 HET SO4 A 322 5 SULFATE 1GDH 115 HET SO4 B 322 5 SULFATE 1GDH 116 FORMUL 3 SO4 2(O4 S1) 1GDH 117 FORMUL 4 HOH *197(H2 O1) 1GDH 118 HELIX 1 A1 GLU A 13 SER A 22 1 1GDH 119 HELIX 2 A2 ILE A 36 ALA A 43 1 1GDH 120 HELIX 3 A3 LYS A 59 ARG A 64 1 1GDH 121 HELIX 4 A4 LEU A 84 ALA A 89 1 1GDH 122 HELIX 5 AA THR A 102 ALA A 117 1 1GDH 123 HELIX 6 A5 ALA A 120 ARG A 128 1 1GDH 124 HELIX 7 AB SER A 157 GLY A 168 1 1GDH 125 HELIX 8 AC SER A 183 SER A 188 1 1GDH 126 HELIX 9 A6 LEU A 197 SER A 202 1 1GDH 127 HELIX 10 AE LYS A 223 ILE A 226 1 1GDH 128 HELIX 11 AF ASN A 246 ALA A 255 1 1GDH 129 HELIX 12 A7 THR A 293 GLY A 312 1 1GDH 130 HELIX 13 B1 GLU B 13 SER B 22 1 1GDH 131 HELIX 14 B2 ILE B 36 ALA B 43 1 1GDH 132 HELIX 15 B3 LYS B 59 ARG B 64 1 1GDH 133 HELIX 16 B4 LEU B 84 ALA B 89 1 1GDH 134 HELIX 17 BA THR B 102 ALA B 117 1 1GDH 135 HELIX 18 B5 ALA B 120 ARG B 128 1 1GDH 136 HELIX 19 BB SER B 157 GLY B 168 1 1GDH 137 HELIX 20 BC SER B 183 SER B 188 1 1GDH 138 HELIX 21 B6 LEU B 197 SER B 202 1 1GDH 139 HELIX 22 BE LYS B 223 ILE B 226 1 1GDH 140 HELIX 23 BF ASN B 246 ALA B 255 1 1GDH 141 HELIX 24 B7 THR B 293 GLY B 312 1 1GDH 142 SHEET 1 AA 5 ASP A 24 ALA A 27 0 1GDH 143 SHEET 2 AA 5 LYS A 4 ILE A 7 1 1GDH 144 SHEET 3 AA 5 ALA A 48 THR A 52 1 1GDH 145 SHEET 4 AA 5 CYS A 71 TYR A 75 1 1GDH 146 SHEET 5 AA 5 LYS A 93 ASN A 96 1 1GDH 147 SHEET 1 AB 7 ALA A 191 PHE A 193 0 1GDH 148 SHEET 2 AB 7 ASP A 172 PHE A 176 1 1GDH 149 SHEET 3 AB 7 THR A 149 TYR A 153 1 1GDH 150 SHEET 4 AB 7 PHE A 206 LEU A 209 1 1GDH 151 SHEET 5 AB 7 ALA A 233 ASN A 237 1 1GDH 152 SHEET 6 AB 7 LEU A 258 PHE A 263 1 1GDH 153 SHEET 7 AB 7 THR A 282 LEU A 284 1 1GDH 154 SHEET 1 BA 5 ASP B 24 ALA B 27 0 1GDH 155 SHEET 2 BA 5 LYS B 4 ILE B 7 1 1GDH 156 SHEET 3 BA 5 ALA B 48 THR B 52 1 1GDH 157 SHEET 4 BA 5 CYS B 71 TYR B 75 1 1GDH 158 SHEET 5 BA 5 LYS B 93 ASN B 96 1 1GDH 159 SHEET 1 BB 7 ALA B 191 PHE B 193 0 1GDH 160 SHEET 2 BB 7 ASP B 172 PHE B 176 1 1GDH 161 SHEET 3 BB 7 THR B 149 TYR B 153 1 1GDH 162 SHEET 4 BB 7 PHE B 206 LEU B 209 1 1GDH 163 SHEET 5 BB 7 ALA B 233 ASN B 237 1 1GDH 164 SHEET 6 BB 7 LEU B 258 PHE B 263 1 1GDH 165 SHEET 7 BB 7 THR B 282 LEU B 284 1 1GDH 166 CRYST1 60.410 60.530 66.290 102.30 113.73 102.73 P 1 2 1GDH 167 ORIGX1 1.000000 0.000000 0.000000 0.00000 1GDH 168 ORIGX2 0.000000 1.000000 0.000000 0.00000 1GDH 169 ORIGX3 0.000000 0.000000 1.000000 0.00000 1GDH 170 SCALE1 0.016554 0.003740 0.009074 0.00000 1GDH 171 SCALE2 0.000000 0.016937 0.006080 0.00000 1GDH 172 SCALE3 0.000000 0.000000 0.017508 0.00000 1GDH 173 MTRIX1 1 0.350790 -0.491090 0.797360 17.05181 1 1GDH 174 MTRIX2 1 -0.482810 -0.824420 -0.295350 72.93915 1 1GDH 175 MTRIX3 1 0.802400 -0.281360 -0.526300 15.54483 1 1GDH 176