HEADER OXYGEN STORAGE/TRANSPORT 21-JUN-00 1F6H TITLE COMBINED RIETVELD AND STEREOCHEMICAL RESTRAINT REFINEMENT OF A PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYOGLOBIN (MET); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHYSETER CATODON; SOURCE 3 ORGANISM_COMMON: SPERM WHALE; SOURCE 4 ORGANISM_TAXID: 9755 KEYWDS POWDER DIFFRACTION, RIETVELD REFINEMENT, MYOBLOBIN(MET), OXYGEN KEYWDS 2 STORAGE-TRANSPORT COMPLEX EXPDTA POWDER DIFFRACTION AUTHOR R.B.VON DREELE REVDAT 3 07-FEB-24 1F6H 1 REMARK LINK REVDAT 2 24-FEB-09 1F6H 1 VERSN REVDAT 1 21-JUL-00 1F6H 0 JRNL AUTH R.B.VON DREELE JRNL TITL COMBINED RIETVELD AND STEREOCHEMICAL RESTRAINT REFINEMENT OF JRNL TITL 2 A PROTEIN CRYSTAL STRUCTURE JRNL REF J.APPL.CRYSTALLOGR. V. 32 1084 1999 JRNL REFN ISSN 0021-8898 JRNL DOI 10.1107/S002188989901064X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 4 REMARK 4 1F6H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011302. REMARK 250 REMARK 250 EXPERIMENTAL DETAILS REMARK 250 EXPERIMENT TYPE : POWDER DIFFRACTION REMARK 250 DATE OF DATA COLLECTION : 20-MAR-98 REMARK 250 REMARK 250 REMARK: SECOND PHASE OF (NH4)2SO4 IN SAMPLE REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASN A 132 N GLU A 136 2.16 REMARK 500 O HIS A 82 N ALA A 84 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 19 -74.27 -57.36 REMARK 500 LYS A 79 35.82 72.69 REMARK 500 GLU A 83 -29.04 -23.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 31 0.08 SIDE CHAIN REMARK 500 ARG A 45 0.08 SIDE CHAIN REMARK 500 ARG A 118 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 230 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 93 NE2 REMARK 620 2 HEM A 230 NA 71.3 REMARK 620 3 HEM A 230 NB 83.6 88.2 REMARK 620 4 HEM A 230 NC 107.4 177.4 89.4 REMARK 620 5 HEM A 230 ND 96.0 90.8 179.0 91.6 REMARK 620 6 HOH A 231 O 160.5 89.7 91.6 91.4 88.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 230 DBREF 1F6H A 1 153 UNP P02185 MYG_PHYCA 1 153 SEQRES 1 A 153 VAL LEU SER GLU GLY GLU TRP GLN LEU VAL LEU HIS VAL SEQRES 2 A 153 TRP ALA LYS VAL GLU ALA ASP VAL ALA GLY HIS GLY GLN SEQRES 3 A 153 ASP ILE LEU ILE ARG LEU PHE LYS SER HIS PRO GLU THR SEQRES 4 A 153 LEU GLU LYS PHE ASP ARG PHE LYS HIS LEU LYS THR GLU SEQRES 5 A 153 ALA GLU MET LYS ALA SER GLU ASP LEU LYS LYS HIS GLY SEQRES 6 A 153 VAL THR VAL LEU THR ALA LEU GLY ALA ILE LEU LYS LYS SEQRES 7 A 153 LYS GLY HIS HIS GLU ALA GLU LEU LYS PRO LEU ALA GLN SEQRES 8 A 153 SER HIS ALA THR LYS HIS LYS ILE PRO ILE LYS TYR LEU SEQRES 9 A 153 GLU PHE ILE SER GLU ALA ILE ILE HIS VAL LEU HIS SER SEQRES 10 A 153 ARG HIS PRO GLY ASP PHE GLY ALA ASP ALA GLN GLY ALA SEQRES 11 A 153 MET ASN LYS ALA LEU GLU LEU PHE ARG LYS ASP ILE ALA SEQRES 12 A 153 ALA LYS TYR LYS GLU LEU GLY TYR GLN GLY HET HEM A 230 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *(H2 O) HELIX 1 1 ASP A 20 LEU A 29 1 10 HELIX 2 2 LEU A 29 LYS A 34 1 6 HELIX 3 3 PRO A 37 PHE A 43 1 7 HELIX 4 4 ALA A 53 SER A 58 1 6 HELIX 5 5 ASP A 60 LYS A 79 1 20 HELIX 6 6 GLU A 85 HIS A 93 1 9 HELIX 7 7 LYS A 102 HIS A 119 1 18 HELIX 8 8 ASP A 126 ALA A 144 1 19 HELIX 9 9 LYS A 145 GLY A 150 1 6 LINK NE2 HIS A 93 FE HEM A 230 1555 1555 2.93 LINK FE HEM A 230 O HOH A 231 1555 1555 2.06 SITE 1 AC1 13 THR A 39 LYS A 42 PHE A 43 ARG A 45 SITE 2 AC1 13 HIS A 64 THR A 67 VAL A 68 ALA A 71 SITE 3 AC1 13 HIS A 93 ILE A 99 TYR A 103 LEU A 104 SITE 4 AC1 13 ILE A 107 CRYST1 64.411 30.195 34.948 90.00 105.83 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015525 0.000000 0.004403 0.00000 SCALE2 0.000000 0.033118 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029743 0.00000 TER 1218 GLY A 153 HETATM 1219 CHA HEM A 230 16.236 30.495 4.824 1.00 12.98 C HETATM 1220 CHB HEM A 230 13.974 27.473 7.839 1.00 12.98 C HETATM 1221 CHC HEM A 230 13.638 24.208 4.273 1.00 12.98 C HETATM 1222 CHD HEM A 230 15.893 27.244 1.272 1.00 12.98 C HETATM 1223 C1A HEM A 230 15.637 29.979 5.953 1.00 12.98 C HETATM 1224 C2A HEM A 230 15.512 30.640 7.242 1.00 12.98 C HETATM 1225 C3A HEM A 230 14.891 29.801 8.067 1.00 12.98 C HETATM 1226 C4A HEM A 230 14.602 28.590 7.326 1.00 12.98 C HETATM 1227 CMA HEM A 230 14.488 29.967 9.546 1.00 12.98 C HETATM 1228 CAA HEM A 230 16.030 32.078 7.469 1.00 12.98 C HETATM 1229 CBA HEM A 230 15.082 33.261 7.418 1.00 12.98 C HETATM 1230 CGA HEM A 230 15.094 34.271 6.309 1.00 12.98 C HETATM 1231 O1A HEM A 230 14.020 34.361 5.644 1.00 12.98 O HETATM 1232 O2A HEM A 230 16.101 35.009 6.101 1.00 12.98 O HETATM 1233 C1B HEM A 230 13.702 26.323 7.125 1.00 12.98 C HETATM 1234 C2B HEM A 230 13.039 25.148 7.658 1.00 12.98 C HETATM 1235 C3B HEM A 230 12.948 24.250 6.674 1.00 12.98 C HETATM 1236 C4B HEM A 230 13.553 24.842 5.492 1.00 12.98 C HETATM 1237 CMB HEM A 230 12.587 25.062 9.134 1.00 12.98 C HETATM 1238 CAB HEM A 230 12.837 22.706 6.764 1.00 12.98 C HETATM 1239 CBB HEM A 230 13.281 22.075 7.854 1.00 12.98 C HETATM 1240 C1C HEM A 230 14.208 24.748 3.143 1.00 12.98 C HETATM 1241 C2C HEM A 230 14.299 24.085 1.864 1.00 12.98 C HETATM 1242 C3C HEM A 230 14.923 24.919 1.027 1.00 12.98 C HETATM 1243 C4C HEM A 230 15.243 26.129 1.750 1.00 12.98 C HETATM 1244 CMC HEM A 230 13.750 22.673 1.581 1.00 12.98 C HETATM 1245 CAC HEM A 230 15.017 24.754 -0.504 1.00 12.98 C HETATM 1246 CBC HEM A 230 15.846 25.533 -1.200 1.00 12.98 C HETATM 1247 C1D HEM A 230 16.211 28.398 1.959 1.00 12.98 C HETATM 1248 C2D HEM A 230 16.907 29.562 1.444 1.00 12.98 C HETATM 1249 C3D HEM A 230 17.014 30.474 2.422 1.00 12.98 C HETATM 1250 C4D HEM A 230 16.377 29.904 3.591 1.00 12.98 C HETATM 1251 CMD HEM A 230 17.437 29.648 -0.005 1.00 12.98 C HETATM 1252 CAD HEM A 230 17.683 31.863 2.390 1.00 12.98 C HETATM 1253 CBD HEM A 230 18.899 32.223 3.219 1.00 12.98 C HETATM 1254 CGD HEM A 230 19.225 33.673 3.458 1.00 12.98 C HETATM 1255 O1D HEM A 230 19.708 34.349 2.510 1.00 12.98 O HETATM 1256 O2D HEM A 230 19.015 34.160 4.606 1.00 12.98 O HETATM 1257 NA HEM A 230 15.069 28.725 6.029 1.00 12.98 N HETATM 1258 NB HEM A 230 14.012 26.107 5.790 1.00 12.98 N HETATM 1259 NC HEM A 230 14.792 25.995 3.048 1.00 12.98 N HETATM 1260 ND HEM A 230 15.906 28.647 3.279 1.00 12.98 N HETATM 1261 FE HEM A 230 14.966 27.375 4.512 1.00 12.98 FE HETATM 1262 O HOH A 231 16.807 26.636 5.059 1.00 12.98 O CONECT 740 1261 CONECT 1219 1223 1250 CONECT 1220 1226 1233 CONECT 1221 1236 1240 CONECT 1222 1243 1247 CONECT 1223 1219 1224 1257 CONECT 1224 1223 1225 1228 CONECT 1225 1224 1226 1227 CONECT 1226 1220 1225 1257 CONECT 1227 1225 CONECT 1228 1224 1229 CONECT 1229 1228 1230 CONECT 1230 1229 1231 1232 CONECT 1231 1230 CONECT 1232 1230 CONECT 1233 1220 1234 1258 CONECT 1234 1233 1235 1237 CONECT 1235 1234 1236 1238 CONECT 1236 1221 1235 1258 CONECT 1237 1234 CONECT 1238 1235 1239 CONECT 1239 1238 CONECT 1240 1221 1241 1259 CONECT 1241 1240 1242 1244 CONECT 1242 1241 1243 1245 CONECT 1243 1222 1242 1259 CONECT 1244 1241 CONECT 1245 1242 1246 CONECT 1246 1245 CONECT 1247 1222 1248 1260 CONECT 1248 1247 1249 1251 CONECT 1249 1248 1250 1252 CONECT 1250 1219 1249 1260 CONECT 1251 1248 CONECT 1252 1249 1253 CONECT 1253 1252 1254 CONECT 1254 1253 1255 1256 CONECT 1255 1254 CONECT 1256 1254 CONECT 1257 1223 1226 1261 CONECT 1258 1233 1236 1261 CONECT 1259 1240 1243 1261 CONECT 1260 1247 1250 1261 CONECT 1261 740 1257 1258 1259 CONECT 1261 1260 1262 CONECT 1262 1261 MASTER 101 0 1 9 0 0 4 6 1261 1 46 12 END