HEADER OXIDOREDUCTASE 05-MAY-16 5JQR TITLE THE STRUCTURE OF ASCORBATE PEROXIDASE COMPOUND II FORMED BY REACTION TITLE 2 WITH M-CPBA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ASCORBATE PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOSOLIC ASCORBATE PEROXIDASE 1; 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME PEROXIDASE, INTERMEDIATES, COMPOUND II, FERRYL, MULTICRYSTAL, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.KWON,E.L.RAVEN,P.C.E.MOODY REVDAT 3 10-JAN-24 5JQR 1 REMARK REVDAT 2 30-AUG-17 5JQR 1 ATOM REVDAT 1 21-DEC-16 5JQR 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 : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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) : 58.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 22667 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1190 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1526 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1905 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 401 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.20000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.120 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.128 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.781 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2031 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1891 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2771 ; 1.979 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4382 ; 1.131 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 252 ; 5.984 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 86 ;36.277 ;24.302 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 318 ;13.858 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;22.656 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 287 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2315 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 450 ; 0.014 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1002 ; 1.468 ; 1.299 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1001 ; 1.450 ; 1.297 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1253 ; 2.100 ; 1.938 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1254 ; 2.099 ; 1.941 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1029 ; 2.167 ; 1.489 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1019 ; 2.073 ; 1.462 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1505 ; 3.199 ; 2.099 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2848 ; 6.954 ;12.670 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2603 ; 6.119 ;11.296 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JQR 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_1000221033. 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 : NULL 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 : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 58.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 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) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.69000 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 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 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 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 HOH A 500 O HOH A 718 1.57 REMARK 500 OE1 GLN A 13 O HOH A 401 2.00 REMARK 500 NE2 GLN A 13 O HOH A 401 2.00 REMARK 500 O HOH A 552 O HOH A 740 2.06 REMARK 500 O HOH A 552 O HOH A 752 2.06 REMARK 500 O HOH A 473 O HOH A 560 2.13 REMARK 500 O3 SO4 A 303 O HOH A 402 2.16 REMARK 500 O HOH A 581 O HOH A 753 2.17 REMARK 500 O1 SO4 A 304 O HOH A 403 2.17 REMARK 500 O HOH A 534 O HOH A 749 2.18 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 HOH A 694 O HOH A 694 7646 0.56 REMARK 500 O HOH A 461 O HOH A 461 7646 0.56 REMARK 500 O HOH A 417 O HOH A 417 2765 1.40 REMARK 500 O HOH A 636 O HOH A 636 2765 1.63 REMARK 500 O HOH A 420 O HOH A 543 2765 2.16 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 ASP A 75 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 133 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 133 CB - CG - OD2 ANGL. DEV. = -5.7 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 -83.71 -100.73 REMARK 500 ASP A 249 87.96 81.72 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 797 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 798 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 799 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A 800 DISTANCE = 6.57 ANGSTROMS REMARK 525 HOH A 801 DISTANCE = 7.03 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 91.6 REMARK 620 3 HEM A 301 NB 88.6 90.8 REMARK 620 4 HEM A 301 NC 87.0 178.6 89.0 REMARK 620 5 HEM A 301 ND 91.4 88.7 179.5 91.5 REMARK 620 6 HOH A 477 O 179.1 89.3 91.7 92.1 88.3 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 67.6 REMARK 620 3 THR A 180 OG1 67.3 103.3 REMARK 620 4 ASN A 182 O 95.1 160.9 75.7 REMARK 620 5 ASN A 182 OD1 139.4 132.6 73.2 65.9 REMARK 620 6 ILE A 185 O 90.2 95.6 141.5 75.7 116.6 REMARK 620 7 ASP A 187 OD1 126.0 59.3 132.7 135.1 87.9 85.7 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 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JPR RELATED DB: PDB REMARK 900 RELATED ID: 2XIF RELATED DB: PDB DBREF 5JQR A 2 250 UNP Q43758 Q43758_SOYBN 2 250 SEQRES 1 A 249 GLY LYS SER TYR PRO THR VAL SER ALA ASP TYR GLN LYS SEQRES 2 A 249 ALA VAL GLU LYS ALA LYS LYS LYS LEU ARG GLY PHE ILE SEQRES 3 A 249 ALA GLU LYS ARG CYS ALA PRO LEU MET LEU ARG LEU ALA SEQRES 4 A 249 TRP HIS SER ALA GLY THR PHE ASP LYS GLY THR LYS THR SEQRES 5 A 249 GLY GLY PRO PHE GLY THR ILE LYS HIS PRO ALA GLU LEU SEQRES 6 A 249 ALA HIS SER ALA ASN ASN GLY LEU ASP ILE ALA VAL ARG SEQRES 7 A 249 LEU LEU GLU PRO LEU LYS ALA GLU PHE PRO ILE LEU SER SEQRES 8 A 249 TYR ALA ASP PHE TYR GLN LEU ALA GLY VAL VAL ALA VAL SEQRES 9 A 249 GLU VAL THR GLY GLY PRO GLU VAL PRO PHE HIS PRO GLY SEQRES 10 A 249 ARG GLU ASP LYS PRO GLU PRO PRO PRO GLU GLY ARG LEU SEQRES 11 A 249 PRO ASP ALA THR LYS GLY SER ASP HIS LEU ARG ASP VAL SEQRES 12 A 249 PHE GLY LYS ALA MET GLY LEU THR ASP GLN ASP ILE VAL SEQRES 13 A 249 ALA LEU SER GLY GLY HIS THR ILE GLY ALA ALA HIS LYS SEQRES 14 A 249 GLU ARG SER GLY PHE GLU GLY PRO TRP THR SER ASN PRO SEQRES 15 A 249 LEU ILE PHE ASP ASN SER TYR PHE THR GLU LEU LEU SER SEQRES 16 A 249 GLY GLU LYS GLU GLY LEU LEU GLN LEU PRO SER ASP LYS SEQRES 17 A 249 ALA LEU LEU SER ASP PRO VAL PHE ARG PRO LEU VAL ASP SEQRES 18 A 249 LYS TYR ALA ALA ASP GLU ASP ALA PHE PHE ALA ASP TYR SEQRES 19 A 249 ALA GLU ALA HIS GLN LYS LEU SER GLU LEU GLY PHE ALA SEQRES 20 A 249 ASP ALA HET HEM A 301 43 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 HOH *401(H2 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 GLU A 87 1 15 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 2.12 LINK O THR A 164 K K A 302 1555 1555 2.67 LINK OG1 THR A 164 K K A 302 1555 1555 3.05 LINK OG1 THR A 180 K K A 302 1555 1555 2.92 LINK O ASN A 182 K K A 302 1555 1555 2.83 LINK OD1 ASN A 182 K K A 302 1555 1555 2.74 LINK O ILE A 185 K K A 302 1555 1555 2.57 LINK OD1 ASP A 187 K K A 302 1555 1555 3.01 LINK FE HEM A 301 O HOH A 477 1555 1555 1.88 SITE 1 AC1 22 PRO A 34 TRP A 41 PRO A 132 ALA A 134 SITE 2 AC1 22 PHE A 145 LEU A 159 HIS A 163 ILE A 165 SITE 3 AC1 22 GLY A 166 ALA A 167 ALA A 168 HIS A 169 SITE 4 AC1 22 ARG A 172 SER A 173 TRP A 179 LEU A 205 SITE 5 AC1 22 SER A 207 TYR A 235 HOH A 424 HOH A 434 SITE 6 AC1 22 HOH A 477 HOH A 510 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 HOH A 402 HOH A 414 SITE 2 AC3 6 HOH A 416 HOH A 553 SITE 1 AC4 8 LYS A 136 GLY A 137 SER A 138 ASP A 139 SITE 2 AC4 8 HIS A 140 HOH A 403 HOH A 404 HOH A 648 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