HEADER OXIDOREDUCTASE 04-MAY-16 5JPR TITLE NEUTRON STRUCTURE OF COMPOUND II OF ASCORBATE PEROXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASCORBATE PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOSOLIC ASCORBATE PEROXIDASE 1,UNCHARACTERIZED PROTEIN; COMPND 5 EC: 1.11.1.11; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 GENE: APX1, GLYMA_U021900; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HEME PEROXIDASE, INTERMEDIATE, FERRYLE HEME, COMPOUND II, CRYO- KEYWDS 2 TRAPPING, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR H.KWON,M.P.BLAKELEY,E.L.RAVEN,P.C.E.MOODY REVDAT 7 01-MAY-24 5JPR 1 REMARK REVDAT 6 16-OCT-19 5JPR 1 REMARK REVDAT 5 06-MAR-19 5JPR 1 REMARK REVDAT 4 14-NOV-18 5JPR 1 REMARK REVDAT 3 03-OCT-18 5JPR 1 SOURCE REMARK ATOM REVDAT 2 30-AUG-17 5JPR 1 ATOM REVDAT 1 21-DEC-16 5JPR 0 JRNL AUTH H.KWON,J.BASRAN,C.M.CASADEI,A.J.FIELDING,T.E.SCHRADER, JRNL AUTH 2 A.OSTERMANN,J.M.DEVOS,P.ALLER,M.P.BLAKELEY,P.C.MOODY, JRNL AUTH 3 E.L.RAVEN JRNL TITL DIRECT VISUALIZATION OF A FE(IV)-OH INTERMEDIATE IN A HEME JRNL TITL 2 ENZYME. JRNL REF NAT COMMUN V. 7 13445 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27897163 JRNL DOI 10.1038/NCOMMS13445 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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 X-RAY DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 23857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1194 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 19.9100 - 3.7485 0.99 2700 143 0.1560 0.2037 REMARK 3 2 3.7485 - 2.9785 0.99 2575 137 0.1459 0.1956 REMARK 3 3 2.9785 - 2.6029 0.99 2514 131 0.1565 0.2102 REMARK 3 4 2.6029 - 2.3654 0.99 2521 134 0.1521 0.2400 REMARK 3 5 2.3654 - 2.1960 0.99 2514 131 0.1536 0.2409 REMARK 3 6 2.1960 - 2.0667 1.00 2500 131 0.1501 0.2111 REMARK 3 7 2.0667 - 1.9633 1.00 2515 133 0.1471 0.2100 REMARK 3 8 1.9633 - 1.8779 0.99 2470 130 0.1657 0.2303 REMARK 3 9 1.8779 - 1.8060 0.94 2354 124 0.1913 0.2599 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.43 REMARK 3 B_SOL : 34.83 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48890 REMARK 3 B22 (A**2) : 0.48890 REMARK 3 B33 (A**2) : -0.97780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.016 4845 REMARK 3 ANGLE : 1.366 8082 REMARK 3 CHIRALITY : 0.115 280 REMARK 3 PLANARITY : 0.009 850 REMARK 3 DIHEDRAL : 11.898 1174 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 3 NEUTRON DATA. REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 68.1 REMARK 3 NUMBER OF REFLECTIONS : 9220 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.310 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 462 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 36.7100 - 3.1756 0.89 3966 209 0.1987 0.2735 REMARK 3 2 3.1756 - 2.5207 0.65 2768 147 0.2399 0.3360 REMARK 3 3 2.5207 - 2.2021 0.48 2024 106 0.3609 0.3918 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.60 REMARK 3 K_SOL : 0.43 REMARK 3 B_SOL : 34.83 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.400 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48890 REMARK 3 B22 (A**2) : 0.48890 REMARK 3 B33 (A**2) : -0.97780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.016 4845 REMARK 3 ANGLE : 1.366 8082 REMARK 3 CHIRALITY : 0.115 280 REMARK 3 PLANARITY : 0.009 850 REMARK 3 DIHEDRAL : 11.898 1174 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 5JPR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000221018. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 - 8.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MULTILAYER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23857 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2XIF REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 14-OCT-15 REMARK 230 TEMPERATURE (KELVIN) : 100.0 REMARK 230 PH : 8.3 - 8.9 REMARK 230 NUMBER OF CRYSTALS USED : NULL REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : LADI III REMARK 230 WAVELENGTH OR RANGE (A) : 3.2 - 4.2 REMARK 230 MONOCHROMATOR : NULL REMARK 230 OPTICS : MULTILAYER REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : MAATEL IMAGINE REMARK 230 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 230 DATA SCALING SOFTWARE : AIMLESS REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 9220 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 230 RESOLUTION RANGE LOW (A) : 40.000 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 69.8 REMARK 230 DATA REDUNDANCY : 4.000 REMARK 230 R MERGE (I) : 0.18000 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 7.0000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 230 COMPLETENESS FOR SHELL (%) : NULL REMARK 230 DATA REDUNDANCY IN SHELL : NULL REMARK 230 R MERGE FOR SHELL (I) : NULL REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : NULL REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : PHASER REMARK 230 STARTING MODEL: 2XIF REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.25 M LITHIUM SULFATE, 0.1 M HEPES PH REMARK 280 8.3 - 8.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z 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 0.000000 -1.000000 0.000000 41.04750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.04750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.58100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.04750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.04750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.58100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.04750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.04750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.58100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.04750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.04750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.58100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 O DOD A 435 LIES ON A SPECIAL POSITION. REMARK 375 O DOD A 565 LIES ON A SPECIAL POSITION. REMARK 375 O DOD A 697 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 MET A -10 REMARK 465 ARG A -9 REMARK 465 GLY A -8 REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 ALA A 250 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 GLY A 110 O DOD A 401 1.39 REMARK 500 O ASP A 187 D2 DOD A 409 1.44 REMARK 500 O DOD A 426 D1 DOD A 707 1.51 REMARK 500 O DOD A 401 O DOD A 501 1.51 REMARK 500 O GLY A 110 D1 DOD A 401 1.56 REMARK 500 O GLY A 110 D2 DOD A 401 1.56 REMARK 500 O3 SO4 A 303 O DOD A 402 1.97 REMARK 500 O DOD A 659 O DOD A 707 2.01 REMARK 500 O DOD A 706 O DOD A 750 2.07 REMARK 500 O DOD A 426 O DOD A 707 2.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O DOD A 421 O DOD A 421 2565 1.54 REMARK 500 O DOD A 628 O DOD A 667 6565 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 79 CZ ARG A 79 NH1 0.080 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 133 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP A 133 CB - CG - OD2 ANGL. DEV. = -6.7 DEGREES 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 ARG A 172 -82.65 -102.39 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 DOD A 783 DISTANCE = 5.85 ANGSTROMS REMARK 525 DOD A 784 DISTANCE = 6.15 ANGSTROMS REMARK 525 DOD A 785 DISTANCE = 6.21 ANGSTROMS REMARK 525 DOD A 786 DISTANCE = 6.33 ANGSTROMS REMARK 525 DOD A 787 DISTANCE = 7.08 ANGSTROMS REMARK 525 DOD A 788 DISTANCE = 7.46 ANGSTROMS REMARK 525 DOD A 789 DISTANCE = 7.54 ANGSTROMS REMARK 525 DOD A 790 DISTANCE = 8.17 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 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 163 NE2 REMARK 620 2 HEM A 301 NA 95.5 REMARK 620 3 HEM A 301 NB 91.6 93.6 REMARK 620 4 HEM A 301 NC 88.9 173.7 90.7 REMARK 620 5 HEM A 301 ND 93.3 85.2 175.0 90.1 REMARK 620 6 DOD A 451 O 178.8 85.5 89.0 90.0 86.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 302 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 164 O REMARK 620 2 THR A 164 OG1 65.3 REMARK 620 3 THR A 180 OG1 67.7 102.3 REMARK 620 4 ASN A 182 O 95.6 159.1 76.5 REMARK 620 5 ASN A 182 OD1 141.2 134.8 74.8 65.6 REMARK 620 6 ILE A 185 O 89.9 94.7 142.1 75.7 115.3 REMARK 620 7 ASP A 187 OD1 125.0 61.0 134.5 134.2 88.6 83.4 REMARK 620 N 1 2 3 4 5 6 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 304 DBREF 5JPR A 2 250 UNP Q43758 Q43758_SOYBN 2 250 SEQADV 5JPR MET A -10 UNP Q43758 INITIATING METHIONINE SEQADV 5JPR ARG A -9 UNP Q43758 EXPRESSION TAG SEQADV 5JPR GLY A -8 UNP Q43758 EXPRESSION TAG SEQADV 5JPR SER A -7 UNP Q43758 EXPRESSION TAG SEQADV 5JPR HIS A -6 UNP Q43758 EXPRESSION TAG SEQADV 5JPR HIS A -5 UNP Q43758 EXPRESSION TAG SEQADV 5JPR HIS A -4 UNP Q43758 EXPRESSION TAG SEQADV 5JPR HIS A -3 UNP Q43758 EXPRESSION TAG SEQADV 5JPR HIS A -2 UNP Q43758 EXPRESSION TAG SEQADV 5JPR HIS A -1 UNP Q43758 EXPRESSION TAG SEQADV 5JPR GLY A 0 UNP Q43758 EXPRESSION TAG SEQADV 5JPR SER A 1 UNP Q43758 EXPRESSION TAG SEQRES 1 A 261 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLY SEQRES 2 A 261 LYS SER TYR PRO THR VAL SER ALA ASP TYR GLN LYS ALA SEQRES 3 A 261 VAL GLU LYS ALA LYS LYS LYS LEU ARG GLY PHE ILE ALA SEQRES 4 A 261 GLU LYS ARG CYS ALA PRO LEU MET LEU ARG LEU ALA TRP SEQRES 5 A 261 HIS SER ALA GLY THR PHE ASP LYS GLY THR LYS THR GLY SEQRES 6 A 261 GLY PRO PHE GLY THR ILE LYS HIS PRO ALA GLU LEU ALA SEQRES 7 A 261 HIS SER ALA ASN ASN GLY LEU ASP ILE ALA VAL ARG LEU SEQRES 8 A 261 LEU GLU PRO LEU LYS ALA GLU PHE PRO ILE LEU SER TYR SEQRES 9 A 261 ALA ASP PHE TYR GLN LEU ALA GLY VAL VAL ALA VAL GLU SEQRES 10 A 261 VAL THR GLY GLY PRO GLU VAL PRO PHE HIS PRO GLY ARG SEQRES 11 A 261 GLU ASP LYS PRO GLU PRO PRO PRO GLU GLY ARG LEU PRO SEQRES 12 A 261 ASP ALA THR LYS GLY SER ASP HIS LEU ARG ASP VAL PHE SEQRES 13 A 261 GLY LYS ALA MET GLY LEU THR ASP GLN ASP ILE VAL ALA SEQRES 14 A 261 LEU SER GLY GLY HIS THR ILE GLY ALA ALA HIS LYS GLU SEQRES 15 A 261 ARG SER GLY PHE GLU GLY PRO TRP THR SER ASN PRO LEU SEQRES 16 A 261 ILE PHE ASP ASN SER TYR PHE THR GLU LEU LEU SER GLY SEQRES 17 A 261 GLU LYS GLU GLY LEU LEU GLN LEU PRO SER ASP LYS ALA SEQRES 18 A 261 LEU LEU SER ASP PRO VAL PHE ARG PRO LEU VAL ASP LYS SEQRES 19 A 261 TYR ALA ALA ASP GLU ASP ALA PHE PHE ALA ASP TYR ALA SEQRES 20 A 261 GLU ALA HIS GLN LYS LEU SER GLU LEU GLY PHE ALA ASP SEQRES 21 A 261 ALA HET HEM A 301 73 HET K A 302 1 HET SO4 A 303 5 HET SO4 A 304 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM K POTASSIUM ION HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 K K 1+ FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 DOD *390(D2 O) HELIX 1 AA1 SER A 9 ARG A 31 1 23 HELIX 2 AA2 CYS A 32 GLY A 45 1 14 HELIX 3 AA3 GLY A 58 LYS A 61 5 4 HELIX 4 AA4 HIS A 62 ALA A 67 1 6 HELIX 5 AA5 HIS A 68 ASN A 72 5 5 HELIX 6 AA6 GLY A 73 ALA A 86 1 14 HELIX 7 AA7 SER A 92 THR A 108 1 17 HELIX 8 AA8 GLY A 137 GLY A 146 1 10 HELIX 9 AA9 THR A 152 GLY A 161 1 10 HELIX 10 AB1 GLY A 162 ILE A 165 5 4 HELIX 11 AB2 ASN A 188 GLY A 197 1 10 HELIX 12 AB3 LEU A 205 ASP A 214 1 10 HELIX 13 AB4 VAL A 216 ASP A 227 1 12 HELIX 14 AB5 ASP A 227 GLU A 244 1 18 SHEET 1 AA1 2 ALA A 167 ALA A 168 0 SHEET 2 AA1 2 GLY A 177 PRO A 178 -1 O GLY A 177 N ALA A 168 LINK NE2 HIS A 163 FE HEM A 301 1555 1555 1.97 LINK O THR A 164 K K A 302 1555 1555 2.73 LINK OG1 THR A 164 K K A 302 1555 1555 3.04 LINK OG1 THR A 180 K K A 302 1555 1555 2.89 LINK O ASN A 182 K K A 302 1555 1555 2.80 LINK OD1 ASN A 182 K K A 302 1555 1555 2.78 LINK O ILE A 185 K K A 302 1555 1555 2.65 LINK OD1 ASP A 187 K K A 302 1555 1555 2.95 LINK FE HEM A 301 O DOD A 451 1555 1555 1.88 SITE 1 AC1 25 PRO A 34 TRP A 41 PRO A 132 ALA A 134 SITE 2 AC1 25 LEU A 141 PHE A 145 LEU A 159 SER A 160 SITE 3 AC1 25 GLY A 162 HIS A 163 ILE A 165 GLY A 166 SITE 4 AC1 25 ALA A 167 ALA A 168 HIS A 169 ARG A 172 SITE 5 AC1 25 SER A 173 TRP A 179 LEU A 205 SER A 207 SITE 6 AC1 25 TYR A 235 DOD A 425 DOD A 434 DOD A 451 SITE 7 AC1 25 DOD A 477 SITE 1 AC2 5 THR A 164 THR A 180 ASN A 182 ILE A 185 SITE 2 AC2 5 ASP A 187 SITE 1 AC3 6 PRO A 127 ARG A 130 DOD A 402 DOD A 404 SITE 2 AC3 6 DOD A 471 DOD A 570 SITE 1 AC4 7 LYS A 136 GLY A 137 SER A 138 ASP A 139 SITE 2 AC4 7 HIS A 140 DOD A 403 DOD A 590 CRYST1 82.095 82.095 75.162 90.00 90.00 90.00 P 42 21 2 8 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 0.012181 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012181 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013305 0.00000