HEADER OXIDOREDUCTASE 06-MAR-25 9QDT TITLE CYTOCHROME C PEROXIDASE YHJA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE CYTOCHROME C PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: YHJA, B3518, JW3486; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CYTOCHROME C, PEROXIDASE, MULTIHEME PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR O.EINSLE,A.WUEST REVDAT 2 13-AUG-25 9QDT 1 JRNL REVDAT 1 30-JUL-25 9QDT 0 JRNL AUTH P.HEWITT,J.SEIDEL,A.WUST,M.SMITH,S.J.MAIOCCO,S.SHTERNBERG, JRNL AUTH 2 M.HOFFMANN,T.SPATZAL,S.GERHARDT,O.EINSLE,S.J.ELLIOTT JRNL TITL ESCHERICHIA COLI TRIHEME ENZYME YHJA: STRUCTURE AND JRNL TITL 2 REACTIVITY. JRNL REF BIOCHEMISTRY V. 64 3322 2025 JRNL REFN ISSN 0006-2960 JRNL PMID 40669070 JRNL DOI 10.1021/ACS.BIOCHEM.5C00202 REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 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) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22976 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 : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.158 REMARK 3 FREE R VALUE TEST SET COUNT : 1185 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) : 2.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1583 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3268 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 152 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.26600 REMARK 3 B22 (A**2) : -0.26600 REMARK 3 B33 (A**2) : 0.53300 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): 0.299 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.232 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.179 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 17.741 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3517 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3242 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4816 ; 1.954 ; 1.892 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7474 ; 0.644 ; 1.798 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 416 ; 7.175 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 17 ; 7.899 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 557 ;18.428 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 490 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4164 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 812 ; 0.010 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 858 ; 0.298 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 62 ; 0.141 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1731 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 95 ; 0.169 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.016 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 8 ; 0.071 ; 0.200 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): 1667 ; 2.919 ; 3.815 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1667 ; 2.919 ; 3.815 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2082 ; 4.371 ; 6.860 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2083 ; 4.371 ; 6.862 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1850 ; 3.752 ; 4.155 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1844 ; 3.648 ; 4.141 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2734 ; 5.775 ; 7.463 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2729 ; 5.638 ; 7.442 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : MASK BULK SOLVENT 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: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9QDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAR-25. REMARK 100 THE DEPOSITION ID IS D_1292146114. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9393 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23032 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.570 REMARK 200 RESOLUTION RANGE LOW (A) : 82.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 15.40 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 15.20 REMARK 200 R MERGE FOR SHELL (I) : 1.36300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: NULL REMARK 200 REMARK 200 REMARK: OCTAGON REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M NA/K TARTRATE 100 MM HEPES/NAOH REMARK 280 2.5 MM NA2S2O4, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 67.34000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.71000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.71000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.67000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.71000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.71000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.01000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.71000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.71000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.67000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.71000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.71000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 101.01000 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 67.34000 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: 4360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 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 619 LIES ON A SPECIAL POSITION. 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 CE MET A 429 FE HEC A 502 1.78 REMARK 500 CE MET A 429 NB HEC A 502 1.87 REMARK 500 SG CYS A 210 CAC HEC A 501 2.06 REMARK 500 O PHE A 293 O VAL A 296 2.09 REMARK 500 SG CYS A 59 CAB HEM A 503 2.12 REMARK 500 SG CYS A 354 CAC HEC A 502 2.17 REMARK 500 CE MET A 429 NA HEC A 502 2.19 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 202 CB - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 VAL A 218 N - CA - CB ANGL. DEV. = -15.4 DEGREES REMARK 500 GLN A 399 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 ARG A 416 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 416 NE - CZ - NH2 ANGL. DEV. = -5.1 DEGREES REMARK 500 MET A 429 CG - SD - CE ANGL. DEV. = -28.8 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 ALA A 78 23.19 -140.18 REMARK 500 TYR A 159 -40.78 -133.42 REMARK 500 PHE A 249 149.16 83.76 REMARK 500 GLU A 270 -98.88 -115.16 REMARK 500 LEU A 397 -0.70 81.27 REMARK 500 ALA A 411 151.94 -48.02 REMARK 500 PHE A 414 163.01 68.39 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 169 0.09 SIDE CHAIN REMARK 500 ARG A 398 0.08 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 503 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 NE2 REMARK 620 2 HEM A 503 NA 93.7 REMARK 620 3 HEM A 503 NB 86.2 86.7 REMARK 620 4 HEM A 503 NC 95.4 169.7 89.1 REMARK 620 5 HEM A 503 ND 98.3 93.6 175.4 89.8 REMARK 620 6 MET A 125 SD 172.7 87.4 86.6 83.0 88.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 505 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 131 O REMARK 620 2 LEU A 133 O 95.8 REMARK 620 3 ALA A 136 O 77.2 79.6 REMARK 620 4 HOH A 622 O 82.9 83.3 152.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 211 NE2 REMARK 620 2 HEC A 501 NA 97.7 REMARK 620 3 HEC A 501 NB 88.7 87.8 REMARK 620 4 HEC A 501 NC 94.4 167.2 88.7 REMARK 620 5 HEC A 501 ND 100.2 91.1 171.1 90.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 504 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 235 OD1 REMARK 620 2 THR A 410 O 142.4 REMARK 620 3 PRO A 412 O 94.3 77.7 REMARK 620 4 HOH A 615 O 78.7 63.8 72.8 REMARK 620 5 HOH A 618 O 69.6 144.2 85.7 140.0 REMARK 620 6 HOH A 621 O 80.6 88.8 150.7 77.9 118.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 355 NE2 REMARK 620 2 HEC A 502 NA 90.5 REMARK 620 3 HEC A 502 NB 82.7 86.9 REMARK 620 4 HEC A 502 NC 93.0 173.0 87.5 REMARK 620 5 HEC A 502 ND 100.3 93.0 176.9 92.3 REMARK 620 6 MET A 429 SD 178.6 90.7 96.8 85.7 80.2 REMARK 620 N 1 2 3 4 5 DBREF 9QDT A 46 462 UNP P37197 YHJA_ECOLI 46 462 SEQRES 1 A 417 GLU ASN ASN LYS VAL LEU GLY PHE LEU ARG GLU LYS GLY SEQRES 2 A 417 CYS ASP TYR CYS HIS THR PRO SER ALA GLU LEU PRO ALA SEQRES 3 A 417 TYR TYR TYR ILE PRO GLY ALA LYS GLN LEU MET ASP TYR SEQRES 4 A 417 ASP ILE LYS LEU GLY TYR LYS SER PHE ASN LEU GLU ALA SEQRES 5 A 417 VAL ARG ALA ALA LEU LEU ALA ASP LYS PRO VAL SER GLN SEQRES 6 A 417 SER ASP LEU ASN LYS ILE GLU TRP VAL MET GLN TYR GLU SEQRES 7 A 417 THR MET PRO PRO THR ARG TYR THR ALA LEU HIS TRP ALA SEQRES 8 A 417 GLY LYS VAL SER ASP GLU GLU ARG ALA GLU ILE LEU ALA SEQRES 9 A 417 TRP ILE ALA LYS GLN ARG ALA GLU TYR TYR ALA SER ASN SEQRES 10 A 417 ASP THR ALA PRO GLU HIS ARG ASN GLU PRO VAL GLN PRO SEQRES 11 A 417 ILE PRO GLN LYS LEU PRO THR ASP ALA GLN LYS VAL ALA SEQRES 12 A 417 LEU GLY PHE ALA LEU TYR HIS ASP PRO ARG LEU SER ALA SEQRES 13 A 417 ASP SER THR ILE SER CYS ALA HIS CYS HIS ALA LEU ASN SEQRES 14 A 417 ALA GLY GLY VAL ASP GLY ARG LYS THR SER ILE GLY VAL SEQRES 15 A 417 GLY GLY ALA VAL GLY PRO ILE ASN ALA PRO THR VAL PHE SEQRES 16 A 417 ASN SER VAL PHE ASN VAL GLU GLN PHE TRP ASP GLY ARG SEQRES 17 A 417 ALA ALA THR LEU GLN ASP GLN ALA GLY GLY PRO PRO LEU SEQRES 18 A 417 ASN PRO ILE GLU MET ALA SER LYS SER TRP ASP GLU ILE SEQRES 19 A 417 ILE ALA LYS LEU GLU LYS ASP PRO GLN LEU LYS THR GLN SEQRES 20 A 417 PHE LEU GLU VAL TYR PRO GLN GLY PHE SER GLY GLU ASN SEQRES 21 A 417 ILE THR ASP ALA ILE ALA GLU PHE GLU LYS THR LEU ILE SEQRES 22 A 417 THR PRO ASP SER PRO PHE ASP LYS TRP LEU ARG GLY ASP SEQRES 23 A 417 GLU ASN ALA LEU THR ALA GLN GLN LYS LYS GLY TYR GLN SEQRES 24 A 417 LEU PHE LYS ASP ASN LYS CYS ALA THR CYS HIS GLY GLY SEQRES 25 A 417 ILE ILE LEU GLY GLY ARG SER PHE GLU PRO LEU GLY LEU SEQRES 26 A 417 LYS LYS ASP PHE ASN PHE GLY GLU ILE THR ALA ALA ASP SEQRES 27 A 417 ILE GLY ARG MET ASN VAL THR LYS GLU GLU ARG ASP LYS SEQRES 28 A 417 LEU ARG GLN LYS VAL PRO GLY LEU ARG ASN VAL ALA LEU SEQRES 29 A 417 THR ALA PRO TYR PHE HIS ARG GLY ASP VAL PRO THR LEU SEQRES 30 A 417 ASP GLY ALA VAL LYS LEU MET LEU ARG TYR GLN VAL GLY SEQRES 31 A 417 LYS GLU LEU PRO GLN GLU ASP VAL ASP ASP ILE VAL ALA SEQRES 32 A 417 PHE LEU HIS SER LEU ASN GLY VAL TYR THR PRO TYR MET SEQRES 33 A 417 GLN HET HEC A 501 43 HET HEC A 502 43 HET HEM A 503 43 HET CA A 504 1 HET CA A 505 1 HET CL A 506 1 HET EPE A 507 15 HET SO4 A 508 5 HETNAM HEC HEME C HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM SO4 SULFATE ION HETSYN HEM HEME HETSYN EPE HEPES FORMUL 2 HEC 2(C34 H34 FE N4 O4) FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 CA 2(CA 2+) FORMUL 7 CL CL 1- FORMUL 8 EPE C8 H18 N2 O4 S FORMUL 9 SO4 O4 S 2- FORMUL 10 HOH *47(H2 O) HELIX 1 AA1 GLU A 46 LYS A 57 1 12 HELIX 2 AA2 GLY A 58 THR A 64 1 7 HELIX 3 AA3 PRO A 70 TYR A 74 5 5 HELIX 4 AA4 ALA A 78 PHE A 93 1 16 HELIX 5 AA5 ASN A 94 ALA A 104 1 11 HELIX 6 AA6 SER A 109 GLU A 123 1 15 HELIX 7 AA7 PRO A 127 THR A 131 5 5 HELIX 8 AA8 SER A 140 TYR A 159 1 20 HELIX 9 AA9 ALA A 165 ARG A 169 5 5 HELIX 10 AB1 ASP A 183 HIS A 195 1 13 HELIX 11 AB2 ASP A 196 SER A 200 5 5 HELIX 12 AB3 SER A 206 CYS A 210 5 5 HELIX 13 AB4 ALA A 212 GLY A 216 5 5 HELIX 14 AB5 GLY A 226 ALA A 230 5 5 HELIX 15 AB6 ASN A 241 ASN A 245 5 5 HELIX 16 AB7 THR A 256 GLY A 262 1 7 HELIX 17 AB8 GLY A 263 ASN A 267 5 5 HELIX 18 AB9 SER A 275 GLU A 284 1 10 HELIX 19 AC1 ASP A 286 VAL A 296 1 11 HELIX 20 AC2 SER A 302 LYS A 315 1 14 HELIX 21 AC3 SER A 322 ARG A 329 1 8 HELIX 22 AC4 ASP A 331 LEU A 335 5 5 HELIX 23 AC5 THR A 336 ASN A 349 1 14 HELIX 24 AC6 LYS A 350 HIS A 355 1 6 HELIX 25 AC7 THR A 380 GLY A 385 1 6 HELIX 26 AC8 ARG A 386 LYS A 391 1 6 HELIX 27 AC9 GLU A 392 LYS A 396 5 5 HELIX 28 AD1 ASN A 406 THR A 410 5 5 HELIX 29 AD2 THR A 421 GLN A 433 1 13 HELIX 30 AD3 PRO A 439 SER A 452 1 14 SHEET 1 AA1 2 PHE A 365 PRO A 367 0 SHEET 2 AA1 2 ARG A 398 LYS A 400 -1 O GLN A 399 N GLU A 366 LINK SG CYS A 207 CAB HEC A 501 1555 1555 1.96 LINK SG CYS A 351 CAB HEC A 502 1555 1555 1.83 LINK NE2 HIS A 63 FE HEM A 503 1555 1555 1.95 LINK SD MET A 125 FE HEM A 503 1555 1555 2.21 LINK O THR A 131 CA CA A 505 1555 1555 2.62 LINK O LEU A 133 CA CA A 505 1555 1555 2.63 LINK O ALA A 136 CA CA A 505 1555 1555 2.35 LINK NE2 HIS A 211 FE HEC A 501 1555 1555 2.14 LINK OD1 ASN A 235 CA CA A 504 1555 1555 2.40 LINK NE2 HIS A 355 FE HEC A 502 1555 1555 1.97 LINK O THR A 410 CA CA A 504 1555 1555 2.52 LINK O PRO A 412 CA CA A 504 1555 1555 2.38 LINK SD MET A 429 FE HEC A 502 1555 1555 2.50 LINK CA CA A 504 O HOH A 615 1555 1555 2.48 LINK CA CA A 504 O HOH A 618 1555 1555 2.41 LINK CA CA A 504 O HOH A 621 1555 1555 2.40 LINK CA CA A 505 O HOH A 622 1555 3555 2.66 CISPEP 1 MET A 125 PRO A 126 0 -2.92 CISPEP 2 ALA A 411 PRO A 412 0 -9.84 CRYST1 101.420 101.420 134.680 90.00 90.00 90.00 P 41 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 0.009860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007425 0.00000 CONECT 147 3398 CONECT 644 3398 CONECT 693 3400 CONECT 705 3400 CONECT 737 3400 CONECT 1295 3292 CONECT 1326 3270 CONECT 1477 3399 CONECT 2401 3335 CONECT 2429 3313 CONECT 2849 3399 CONECT 2861 3399 CONECT 2997 3313 CONECT 3270 1326 3275 3286 3294 CONECT 3270 3302 CONECT 3271 3276 3306 CONECT 3272 3279 3287 CONECT 3273 3290 3295 CONECT 3274 3298 3303 CONECT 3275 3270 3276 3279 CONECT 3276 3271 3275 3277 CONECT 3277 3276 3278 3281 CONECT 3278 3277 3279 3280 CONECT 3279 3272 3275 3278 CONECT 3280 3278 CONECT 3281 3277 3282 CONECT 3282 3281 3283 CONECT 3283 3282 3284 3285 CONECT 3284 3283 CONECT 3285 3283 CONECT 3286 3270 3287 3290 CONECT 3287 3272 3286 3288 CONECT 3288 3287 3289 3291 CONECT 3289 3288 3290 3292 CONECT 3290 3273 3286 3289 CONECT 3291 3288 CONECT 3292 1295 3289 3293 CONECT 3293 3292 CONECT 3294 3270 3295 3298 CONECT 3295 3273 3294 3296 CONECT 3296 3295 3297 3299 CONECT 3297 3296 3298 3300 CONECT 3298 3274 3294 3297 CONECT 3299 3296 CONECT 3300 3297 3301 CONECT 3301 3300 CONECT 3302 3270 3303 3306 CONECT 3303 3274 3302 3304 CONECT 3304 3303 3305 3307 CONECT 3305 3304 3306 3308 CONECT 3306 3271 3302 3305 CONECT 3307 3304 CONECT 3308 3305 3309 CONECT 3309 3308 3310 CONECT 3310 3309 3311 3312 CONECT 3311 3310 CONECT 3312 3310 CONECT 3313 2429 2997 3318 3329 CONECT 3313 3337 3345 CONECT 3314 3319 3349 CONECT 3315 3322 3330 CONECT 3316 3333 3338 CONECT 3317 3341 3346 CONECT 3318 3313 3319 3322 CONECT 3319 3314 3318 3320 CONECT 3320 3319 3321 3324 CONECT 3321 3320 3322 3323 CONECT 3322 3315 3318 3321 CONECT 3323 3321 CONECT 3324 3320 3325 CONECT 3325 3324 3326 CONECT 3326 3325 3327 3328 CONECT 3327 3326 CONECT 3328 3326 CONECT 3329 3313 3330 3333 CONECT 3330 3315 3329 3331 CONECT 3331 3330 3332 3334 CONECT 3332 3331 3333 3335 CONECT 3333 3316 3329 3332 CONECT 3334 3331 CONECT 3335 2401 3332 3336 CONECT 3336 3335 CONECT 3337 3313 3338 3341 CONECT 3338 3316 3337 3339 CONECT 3339 3338 3340 3342 CONECT 3340 3339 3341 3343 CONECT 3341 3317 3337 3340 CONECT 3342 3339 CONECT 3343 3340 3344 CONECT 3344 3343 CONECT 3345 3313 3346 3349 CONECT 3346 3317 3345 3347 CONECT 3347 3346 3348 3350 CONECT 3348 3347 3349 3351 CONECT 3349 3314 3345 3348 CONECT 3350 3347 CONECT 3351 3348 3352 CONECT 3352 3351 3353 CONECT 3353 3352 3354 3355 CONECT 3354 3353 CONECT 3355 3353 CONECT 3356 3360 3387 CONECT 3357 3363 3370 CONECT 3358 3373 3377 CONECT 3359 3380 3384 CONECT 3360 3356 3361 3394 CONECT 3361 3360 3362 3365 CONECT 3362 3361 3363 3364 CONECT 3363 3357 3362 3394 CONECT 3364 3362 CONECT 3365 3361 3366 CONECT 3366 3365 3367 CONECT 3367 3366 3368 3369 CONECT 3368 3367 CONECT 3369 3367 CONECT 3370 3357 3371 3395 CONECT 3371 3370 3372 3374 CONECT 3372 3371 3373 3375 CONECT 3373 3358 3372 3395 CONECT 3374 3371 CONECT 3375 3372 3376 CONECT 3376 3375 CONECT 3377 3358 3378 3396 CONECT 3378 3377 3379 3381 CONECT 3379 3378 3380 3382 CONECT 3380 3359 3379 3396 CONECT 3381 3378 CONECT 3382 3379 3383 CONECT 3383 3382 CONECT 3384 3359 3385 3397 CONECT 3385 3384 3386 3388 CONECT 3386 3385 3387 3389 CONECT 3387 3356 3386 3397 CONECT 3388 3385 CONECT 3389 3386 3390 CONECT 3390 3389 3391 CONECT 3391 3390 3392 3393 CONECT 3392 3391 CONECT 3393 3391 CONECT 3394 3360 3363 3398 CONECT 3395 3370 3373 3398 CONECT 3396 3377 3380 3398 CONECT 3397 3384 3387 3398 CONECT 3398 147 644 3394 3395 CONECT 3398 3396 3397 CONECT 3399 1477 2849 2861 3436 CONECT 3399 3439 3442 CONECT 3400 693 705 737 CONECT 3402 3403 3407 3411 CONECT 3403 3402 3404 CONECT 3404 3403 3405 CONECT 3405 3404 3406 3408 CONECT 3406 3405 3407 CONECT 3407 3402 3406 CONECT 3408 3405 3409 CONECT 3409 3408 3410 CONECT 3410 3409 CONECT 3411 3402 3412 CONECT 3412 3411 3413 CONECT 3413 3412 3414 3415 3416 CONECT 3414 3413 CONECT 3415 3413 CONECT 3416 3413 CONECT 3417 3418 3419 3420 3421 CONECT 3418 3417 CONECT 3419 3417 CONECT 3420 3417 CONECT 3421 3417 CONECT 3436 3399 CONECT 3439 3399 CONECT 3442 3399 MASTER 401 0 8 30 2 0 0 6 3467 1 171 33 END