HEADER OXYGEN BINDING 19-OCT-21 7VQG TITLE THE X-RAY STRUCTURE OF HUMAN NEUROGLOBIN A15C MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROGLOBIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NGB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NEUROGLOBIN, OXYGEN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Y.W.LIN REVDAT 3 20-NOV-24 7VQG 1 REMARK REVDAT 2 29-NOV-23 7VQG 1 REMARK REVDAT 1 26-OCT-22 7VQG 0 JRNL AUTH Y.W.LIN JRNL TITL THE X-RAY STRUCTURE OF HUMAN NEUROGLOBIN A15C MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.1_3865 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 56648 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 36.5800 - 3.6600 1.00 2704 144 0.1752 0.1888 REMARK 3 2 3.6600 - 2.9100 1.00 2702 149 0.1601 0.1750 REMARK 3 3 2.9100 - 2.5400 1.00 2703 145 0.1489 0.1431 REMARK 3 4 2.5400 - 2.3100 1.00 2692 155 0.1358 0.1345 REMARK 3 5 2.3100 - 2.1400 1.00 2723 140 0.1333 0.1922 REMARK 3 6 2.1400 - 2.0200 1.00 2702 154 0.1310 0.1953 REMARK 3 7 2.0200 - 1.9200 1.00 2704 139 0.1339 0.1676 REMARK 3 8 1.9200 - 1.8300 1.00 2716 129 0.1313 0.1659 REMARK 3 9 1.8300 - 1.7600 1.00 2677 146 0.1293 0.1907 REMARK 3 10 1.7600 - 1.7000 1.00 2705 137 0.1251 0.1864 REMARK 3 11 1.7000 - 1.6500 1.00 2752 157 0.1195 0.1662 REMARK 3 12 1.6500 - 1.6000 1.00 2672 150 0.1171 0.1541 REMARK 3 13 1.6000 - 1.5600 0.99 2668 142 0.1141 0.1583 REMARK 3 14 1.5600 - 1.5200 1.00 2729 134 0.1116 0.1612 REMARK 3 15 1.5200 - 1.4900 1.00 2695 147 0.1116 0.1519 REMARK 3 16 1.4900 - 1.4500 0.99 2671 138 0.1164 0.1579 REMARK 3 17 1.4500 - 1.4300 0.99 2718 151 0.1244 0.1771 REMARK 3 18 1.4300 - 1.4000 0.99 2642 136 0.1296 0.2014 REMARK 3 19 1.4000 - 1.3700 0.98 2666 135 0.1389 0.1983 REMARK 3 20 1.3700 - 1.3500 0.94 2550 129 0.1483 0.2431 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.092 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.539 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.018 1319 REMARK 3 ANGLE : 1.675 1807 REMARK 3 CHIRALITY : 0.103 187 REMARK 3 PLANARITY : 0.011 224 REMARK 3 DIHEDRAL : 22.734 487 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7VQG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1300025185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60134 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 36.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.8300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.86 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1OJ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% V/V 1,4-DIOXANE, 0.1 M MES REMARK 280 MONOHYDRATE PH 6.5, 1.6 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.28050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.32500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.28050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.32500 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 339 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 351 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 423 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 430 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 437 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 149 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 ASP A 81 89.64 -155.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 455 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 456 DISTANCE = 6.57 ANGSTROMS 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 64 NE2 REMARK 620 2 HEM A 201 NA 87.9 REMARK 620 3 HEM A 201 NB 88.4 88.5 REMARK 620 4 HEM A 201 NC 93.2 176.4 88.0 REMARK 620 5 HEM A 201 ND 92.6 92.2 178.8 91.2 REMARK 620 6 HIS A 96 NE2 177.0 89.9 89.5 88.9 89.5 REMARK 620 N 1 2 3 4 5 DBREF 7VQG A 2 149 UNP Q9NPG2 NGB_HUMAN 2 149 SEQADV 7VQG CYS A 15 UNP Q9NPG2 ALA 15 ENGINEERED MUTATION SEQRES 1 A 148 GLU ARG PRO GLU PRO GLU LEU ILE ARG GLN SER TRP ARG SEQRES 2 A 148 CYS VAL SER ARG SER PRO LEU GLU HIS GLY THR VAL LEU SEQRES 3 A 148 PHE ALA ARG LEU PHE ALA LEU GLU PRO ASP LEU LEU PRO SEQRES 4 A 148 LEU PHE GLN TYR ASN CYS ARG GLN PHE SER SER PRO GLU SEQRES 5 A 148 ASP CYS LEU SER SER PRO GLU PHE LEU ASP HIS ILE ARG SEQRES 6 A 148 LYS VAL MET LEU VAL ILE ASP ALA ALA VAL THR ASN VAL SEQRES 7 A 148 GLU ASP LEU SER SER LEU GLU GLU TYR LEU ALA SER LEU SEQRES 8 A 148 GLY ARG LYS HIS ARG ALA VAL GLY VAL LYS LEU SER SER SEQRES 9 A 148 PHE SER THR VAL GLY GLU SER LEU LEU TYR MET LEU GLU SEQRES 10 A 148 LYS CYS LEU GLY PRO ALA PHE THR PRO ALA THR ARG ALA SEQRES 11 A 148 ALA TRP SER GLN LEU TYR GLY ALA VAL VAL GLN ALA MET SEQRES 12 A 148 SER ARG GLY TRP ASP HET HEM A 201 73 HET DIO A 202 14 HET DIO A 203 14 HET MES A 204 25 HET DIO A 205 14 HET SO4 A 206 5 HET SO4 A 207 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM DIO 1,4-DIETHYLENE DIOXIDE HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 DIO 3(C4 H8 O2) FORMUL 5 MES C6 H13 N O4 S FORMUL 7 SO4 2(O4 S 2-) FORMUL 9 HOH *156(H2 O) HELIX 1 AA1 GLU A 5 ARG A 18 1 14 HELIX 2 AA2 SER A 19 GLU A 35 1 17 HELIX 3 AA3 LEU A 38 CYS A 46 1 9 HELIX 4 AA4 SER A 51 SER A 57 1 7 HELIX 5 AA5 SER A 58 ASN A 78 1 21 HELIX 6 AA6 ASP A 81 SER A 84 5 4 HELIX 7 AA7 LEU A 85 VAL A 99 1 15 HELIX 8 AA8 SER A 104 GLY A 122 1 19 HELIX 9 AA9 PRO A 123 PHE A 125 5 3 HELIX 10 AB1 THR A 126 ARG A 146 1 21 SSBOND 1 CYS A 15 CYS A 120 1555 1555 2.02 SSBOND 2 CYS A 46 CYS A 55 1555 1555 2.05 LINK NE2 HIS A 64 FE HEM A 201 1555 1555 2.05 LINK NE2 HIS A 96 FE HEM A 201 1555 1555 2.00 CRYST1 39.093 40.561 84.650 90.00 90.00 90.00 P 2 21 21 4 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 0.025580 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024654 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011813 0.00000