HEADER OXIDOREDUCTASE 14-MAY-19 6RPD TITLE STRUCTURE OF FERROUS KPDYP IN COMPLEX WITH CYANIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: IRON-DEPENDENT PEROXIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PEROXIDASE,PUTATIVE DEFERROCHELATASE/PEROXIDASE YFEX; COMPND 5 EC: 1.11.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: YFEX, AGG09_21550, B1727_13990, B8011_07420, BL102_0001560, SOURCE 5 BN49_3985, BVX91_12125, CEO55_07245, CIT28_09840, CP905_14695, SOURCE 6 PMK1_00271, SAMEA3531778_01640, SM57_03027; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HEME PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.PFANZAGL,J.BEALE,S.HOFBAUER REVDAT 3 24-JAN-24 6RPD 1 REMARK REVDAT 2 07-OCT-20 6RPD 1 JRNL REVDAT 1 02-SEP-20 6RPD 0 JRNL AUTH V.PFANZAGL,J.H.BEALE,H.MICHLITS,D.SCHMIDT,T.GABLER, JRNL AUTH 2 C.OBINGER,K.DJINOVIC-CARUGO,S.HOFBAUER JRNL TITL X-RAY-INDUCED PHOTOREDUCTION OF HEME METAL CENTERS RAPIDLY JRNL TITL 2 INDUCES ACTIVE-SITE PERTURBATIONS IN A PROTEIN-INDEPENDENT JRNL TITL 3 MANNER. JRNL REF J.BIOL.CHEM. V. 295 13488 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32723869 JRNL DOI 10.1074/JBC.RA120.014087 REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 81529 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 4058 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 50 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.52 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.53 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.34 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1631 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2241 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1536 REMARK 3 BIN R VALUE (WORKING SET) : 0.2221 REMARK 3 BIN FREE R VALUE : 0.2575 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.82 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 134 REMARK 3 SOLVENT ATOMS : 560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.21650 REMARK 3 B22 (A**2) : -1.81870 REMARK 3 B33 (A**2) : -0.39780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.33240 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.190 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.082 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.077 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.097 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.075 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 9890 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 17838 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2174 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1655 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 9890 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 610 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : 10 ; 1.000 ; HARMONIC REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 11381 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.12 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.82 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.49 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 13.7576 2.9011 -2.0851 REMARK 3 T TENSOR REMARK 3 T11: -0.0046 T22: -0.0272 REMARK 3 T33: -0.0075 T12: -0.0042 REMARK 3 T13: -0.0031 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.3673 L22: 0.3686 REMARK 3 L33: 0.1573 L12: 0.0098 REMARK 3 L13: 0.0628 L23: -0.0973 REMARK 3 S TENSOR REMARK 3 S11: 0.0092 S12: 0.0152 S13: 0.0386 REMARK 3 S21: -0.0309 S22: -0.0131 S23: 0.0009 REMARK 3 S31: 0.0373 S32: 0.0009 S33: 0.0040 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 24.8139 1.5192 32.2272 REMARK 3 T TENSOR REMARK 3 T11: -0.0172 T22: 0.0021 REMARK 3 T33: -0.0297 T12: 0.0175 REMARK 3 T13: -0.0067 T23: -0.0084 REMARK 3 L TENSOR REMARK 3 L11: 0.4596 L22: 0.1247 REMARK 3 L33: 0.5074 L12: 0.1269 REMARK 3 L13: 0.1979 L23: 0.1724 REMARK 3 S TENSOR REMARK 3 S11: -0.0266 S12: -0.0543 S13: 0.0213 REMARK 3 S21: 0.0231 S22: 0.0078 S23: -0.0049 REMARK 3 S31: 0.0380 S32: -0.0001 S33: 0.0188 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6RPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.991874 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81557 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 40.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.52 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 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: PHENIX REMARK 200 STARTING MODEL: 6FKS REMARK 200 REMARK 200 REMARK: CUBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% W/V PEG 3350, 0.1 M MGCL2, 0.1 M REMARK 280 TRIS-HCL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 37.87000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 PRO A -2 REMARK 465 LEU A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 PRO B -2 REMARK 465 LEU B -1 REMARK 465 GLY B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 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 OE1 GLU B 125 HE ARG B 175 1.55 REMARK 500 FE HEM A 401 C CYN A 407 2.19 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 GLU A 75 CD GLU A 75 OE1 -0.096 REMARK 500 VAL A 188 C PRO A 189 N 0.143 REMARK 500 PRO A 189 N PRO A 189 CA 0.207 REMARK 500 GLN B 3 C VAL B 4 N -0.207 REMARK 500 GLN B 3 C VAL B 4 N -0.218 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 143 CB - CA - C ANGL. DEV. = 12.7 DEGREES REMARK 500 GLY A 144 C - N - CA ANGL. DEV. = -14.5 DEGREES REMARK 500 GLY A 144 C - N - CA ANGL. DEV. = -13.7 DEGREES REMARK 500 PRO A 189 C - N - CA ANGL. DEV. = 12.6 DEGREES REMARK 500 GLN B 3 O - C - N ANGL. DEV. = 10.0 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 SER A 100 -175.90 -170.28 REMARK 500 SER B 100 -175.95 -171.51 REMARK 500 SER B 100 -175.95 -170.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PRO A 189 -10.97 REMARK 500 PRO A 189 -11.21 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 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 215 NE2 REMARK 620 2 HEM A 401 NA 90.6 REMARK 620 3 HEM A 401 NB 91.1 91.4 REMARK 620 4 HEM A 401 NC 90.7 178.1 89.9 REMARK 620 5 HEM A 401 ND 93.7 89.8 175.0 88.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 406 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD2 REMARK 620 2 HOH A 504 O 90.1 REMARK 620 3 HOH A 517 O 90.4 91.9 REMARK 620 4 HOH A 610 O 84.9 91.7 174.1 REMARK 620 5 HOH A 689 O 91.4 178.1 89.2 87.3 REMARK 620 6 HOH A 764 O 169.1 86.0 99.8 85.1 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 215 NE2 REMARK 620 2 HEM B 401 NA 91.4 REMARK 620 3 HEM B 401 NB 92.0 91.7 REMARK 620 4 HEM B 401 NC 92.1 175.9 90.3 REMARK 620 5 HEM B 401 ND 94.2 88.6 173.8 89.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 220 OD2 REMARK 620 2 HOH B 504 O 92.6 REMARK 620 3 HOH B 545 O 88.4 94.2 REMARK 620 4 HOH B 639 O 91.8 94.2 171.6 REMARK 620 5 HOH B 656 O 93.6 173.4 83.8 87.8 REMARK 620 6 HOH B 704 O 177.4 84.9 91.5 88.7 88.9 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYN A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYN B 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FKS RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN DBREF1 6RPD A 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6RPD A A0A0W8ATM9 1 299 DBREF1 6RPD B 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6RPD B A0A0W8ATM9 1 299 SEQADV 6RPD PRO A -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPD LEU A -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPD GLY A 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPD GLY A 300 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPD PRO B -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPD LEU B -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPD GLY B 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPD GLY B 300 UNP A0A0W8ATM EXPRESSION TAG SEQRES 1 A 303 PRO LEU GLY MET SER GLN VAL GLN SER GLY ILE LEU PRO SEQRES 2 A 303 GLU HIS CYS ARG ALA ALA ILE TRP ILE GLU ALA ASN LEU SEQRES 3 A 303 LYS GLY ASP VAL ASN ALA LEU ARG GLU ALA SER LYS ILE SEQRES 4 A 303 PHE VAL ASP ASN VAL ALA THR PHE GLN ALA LYS PHE PRO SEQRES 5 A 303 ASP ALA LYS LEU GLY ALA VAL VAL ALA PHE GLY ASN ASN SEQRES 6 A 303 VAL TRP ARG GLN LEU SER GLY GLY GLU GLY ALA ASP GLU SEQRES 7 A 303 LEU LYS ASP PHE PRO VAL TYR GLY LYS GLY LEU ALA PRO SEQRES 8 A 303 SER THR GLN TYR ASP LEU LEU ILE HIS ILE LEU SER ALA SEQRES 9 A 303 ARG HIS GLU VAL ASN PHE SER VAL ALA GLN ALA ALA LEU SEQRES 10 A 303 ALA ALA PHE GLY ASP ALA ILE ASP VAL LYS GLU GLU ILE SEQRES 11 A 303 HIS GLY PHE ARG TRP VAL GLU GLU ARG ASP LEU SER GLY SEQRES 12 A 303 PHE VAL ASP GLY THR GLU ASN PRO ALA GLY GLU GLU THR SEQRES 13 A 303 ARG ARG GLU VAL ALA VAL ILE LYS ASP GLY VAL ASP ALA SEQRES 14 A 303 GLY GLY SER TYR VAL PHE VAL GLN ARG TRP GLU HIS ASN SEQRES 15 A 303 LEU LYS GLN LEU ASN ARG MET SER VAL PRO ASP GLN GLU SEQRES 16 A 303 MET MET ILE GLY ARG THR LYS ASP ALA ASN GLU GLU ILE SEQRES 17 A 303 ASP GLY ASP GLU ARG PRO VAL THR SER HIS LEU SER ARG SEQRES 18 A 303 VAL ASP LEU LYS GLU ASP GLY LYS GLY LEU LYS ILE VAL SEQRES 19 A 303 ARG GLN SER LEU PRO TYR GLY THR ALA SER GLY THR HIS SEQRES 20 A 303 GLY LEU TYR PHE CYS ALA TYR CYS ALA ARG LEU TYR ASN SEQRES 21 A 303 ILE GLU GLN GLN LEU LEU SER MET PHE GLY ASP THR ASP SEQRES 22 A 303 GLY LYS ARG ASP ALA MET LEU ARG PHE THR LYS PRO VAL SEQRES 23 A 303 THR GLY GLY TYR TYR PHE ALA PRO SER LEU GLU ARG ILE SEQRES 24 A 303 GLN ALA LEU GLY SEQRES 1 B 303 PRO LEU GLY MET SER GLN VAL GLN SER GLY ILE LEU PRO SEQRES 2 B 303 GLU HIS CYS ARG ALA ALA ILE TRP ILE GLU ALA ASN LEU SEQRES 3 B 303 LYS GLY ASP VAL ASN ALA LEU ARG GLU ALA SER LYS ILE SEQRES 4 B 303 PHE VAL ASP ASN VAL ALA THR PHE GLN ALA LYS PHE PRO SEQRES 5 B 303 ASP ALA LYS LEU GLY ALA VAL VAL ALA PHE GLY ASN ASN SEQRES 6 B 303 VAL TRP ARG GLN LEU SER GLY GLY GLU GLY ALA ASP GLU SEQRES 7 B 303 LEU LYS ASP PHE PRO VAL TYR GLY LYS GLY LEU ALA PRO SEQRES 8 B 303 SER THR GLN TYR ASP LEU LEU ILE HIS ILE LEU SER ALA SEQRES 9 B 303 ARG HIS GLU VAL ASN PHE SER VAL ALA GLN ALA ALA LEU SEQRES 10 B 303 ALA ALA PHE GLY ASP ALA ILE ASP VAL LYS GLU GLU ILE SEQRES 11 B 303 HIS GLY PHE ARG TRP VAL GLU GLU ARG ASP LEU SER GLY SEQRES 12 B 303 PHE VAL ASP GLY THR GLU ASN PRO ALA GLY GLU GLU THR SEQRES 13 B 303 ARG ARG GLU VAL ALA VAL ILE LYS ASP GLY VAL ASP ALA SEQRES 14 B 303 GLY GLY SER TYR VAL PHE VAL GLN ARG TRP GLU HIS ASN SEQRES 15 B 303 LEU LYS GLN LEU ASN ARG MET SER VAL PRO ASP GLN GLU SEQRES 16 B 303 MET MET ILE GLY ARG THR LYS ASP ALA ASN GLU GLU ILE SEQRES 17 B 303 ASP GLY ASP GLU ARG PRO VAL THR SER HIS LEU SER ARG SEQRES 18 B 303 VAL ASP LEU LYS GLU ASP GLY LYS GLY LEU LYS ILE VAL SEQRES 19 B 303 ARG GLN SER LEU PRO TYR GLY THR ALA SER GLY THR HIS SEQRES 20 B 303 GLY LEU TYR PHE CYS ALA TYR CYS ALA ARG LEU TYR ASN SEQRES 21 B 303 ILE GLU GLN GLN LEU LEU SER MET PHE GLY ASP THR ASP SEQRES 22 B 303 GLY LYS ARG ASP ALA MET LEU ARG PHE THR LYS PRO VAL SEQRES 23 B 303 THR GLY GLY TYR TYR PHE ALA PRO SER LEU GLU ARG ILE SEQRES 24 B 303 GLN ALA LEU GLY HET HEM A 401 73 HET GOL A 402 14 HET GOL A 403 14 HET GOL A 404 14 HET GOL A 405 14 HET MG A 406 1 HET CYN A 407 2 HET HEM B 401 73 HET GOL B 402 14 HET GOL B 403 14 HET GOL B 404 14 HET MG B 405 1 HET CYN B 406 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM CYN CYANIDE ION HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 GOL 7(C3 H8 O3) FORMUL 8 MG 2(MG 2+) FORMUL 9 CYN 2(C N 1-) FORMUL 16 HOH *560(H2 O) HELIX 1 AA1 ASN A 28 PHE A 48 1 21 HELIX 2 AA2 PRO A 49 LYS A 52 5 4 HELIX 3 AA3 GLY A 60 GLY A 69 1 10 HELIX 4 AA4 TYR A 82 LEU A 86 5 5 HELIX 5 AA5 ARG A 102 GLY A 118 1 17 HELIX 6 AA6 TRP A 132 ARG A 136 5 5 HELIX 7 AA7 GLY A 150 VAL A 159 1 10 HELIX 8 AA8 ASN A 179 ARG A 185 1 7 HELIX 9 AA9 SER A 187 GLY A 196 1 10 HELIX 10 AB1 SER A 214 ASP A 220 1 7 HELIX 11 AB2 ARG A 254 PHE A 266 1 13 HELIX 12 AB3 ASP A 274 ARG A 278 5 5 HELIX 13 AB4 SER A 292 ALA A 298 1 7 HELIX 14 AB5 ASN B 28 PHE B 48 1 21 HELIX 15 AB6 PRO B 49 LYS B 52 5 4 HELIX 16 AB7 GLY B 60 GLY B 69 1 10 HELIX 17 AB8 TYR B 82 LEU B 86 5 5 HELIX 18 AB9 ARG B 102 GLY B 118 1 17 HELIX 19 AC1 TRP B 132 ARG B 136 5 5 HELIX 20 AC2 GLY B 150 VAL B 159 1 10 HELIX 21 AC3 ASN B 179 ARG B 185 1 7 HELIX 22 AC4 SER B 187 GLY B 196 1 10 HELIX 23 AC5 SER B 214 ASP B 220 1 7 HELIX 24 AC6 ARG B 254 PHE B 266 1 13 HELIX 25 AC7 ASP B 274 ARG B 278 5 5 HELIX 26 AC8 SER B 292 ALA B 298 1 7 SHEET 1 AA1 4 GLY A 54 PHE A 59 0 SHEET 2 AA1 4 LEU A 94 SER A 100 -1 O LEU A 95 N ALA A 58 SHEET 3 AA1 4 ALA A 15 LEU A 23 -1 N ILE A 17 O ILE A 98 SHEET 4 AA1 4 ILE A 121 PHE A 130 -1 O LYS A 124 N GLU A 20 SHEET 1 AA2 4 VAL A 231 ARG A 232 0 SHEET 2 AA2 4 HIS A 244 CYS A 252 -1 O TYR A 251 N VAL A 231 SHEET 3 AA2 4 SER A 169 HIS A 178 -1 N TRP A 176 O LEU A 246 SHEET 4 AA2 4 THR A 280 PRO A 282 -1 O LYS A 281 N GLU A 177 SHEET 1 AA3 4 LEU A 235 GLY A 238 0 SHEET 2 AA3 4 HIS A 244 CYS A 252 -1 O TYR A 247 N LEU A 235 SHEET 3 AA3 4 SER A 169 HIS A 178 -1 N TRP A 176 O LEU A 246 SHEET 4 AA3 4 GLY A 286 ALA A 290 -1 O ALA A 290 N SER A 169 SHEET 1 AA4 2 LYS A 222 GLU A 223 0 SHEET 2 AA4 2 LYS A 226 GLY A 227 -1 O LYS A 226 N GLU A 223 SHEET 1 AA5 4 GLY B 54 PHE B 59 0 SHEET 2 AA5 4 LEU B 94 SER B 100 -1 O LEU B 95 N ALA B 58 SHEET 3 AA5 4 ALA B 15 LEU B 23 -1 N ILE B 19 O ILE B 96 SHEET 4 AA5 4 ILE B 121 PHE B 130 -1 O ASP B 122 N ASN B 22 SHEET 1 AA6 4 VAL B 231 ARG B 232 0 SHEET 2 AA6 4 HIS B 244 CYS B 252 -1 O TYR B 251 N VAL B 231 SHEET 3 AA6 4 SER B 169 HIS B 178 -1 N TRP B 176 O LEU B 246 SHEET 4 AA6 4 THR B 280 PRO B 282 -1 O LYS B 281 N GLU B 177 SHEET 1 AA7 4 LEU B 235 GLY B 238 0 SHEET 2 AA7 4 HIS B 244 CYS B 252 -1 O TYR B 247 N LEU B 235 SHEET 3 AA7 4 SER B 169 HIS B 178 -1 N TRP B 176 O LEU B 246 SHEET 4 AA7 4 GLY B 286 ALA B 290 -1 O ALA B 290 N SER B 169 SHEET 1 AA8 2 LYS B 222 GLU B 223 0 SHEET 2 AA8 2 LYS B 226 GLY B 227 -1 O LYS B 226 N GLU B 223 LINK NE2 HIS A 215 FE HEM A 401 1555 1555 2.08 LINK OD2 ASP A 220 MG MG A 406 1555 1555 2.07 LINK MG MG A 406 O HOH A 504 1555 1555 1.96 LINK MG MG A 406 O HOH A 517 1555 1555 2.00 LINK MG MG A 406 O HOH A 610 1555 1555 2.01 LINK MG MG A 406 O HOH A 689 1555 1555 2.01 LINK MG MG A 406 O HOH A 764 1555 1555 2.03 LINK NE2 HIS B 215 FE HEM B 401 1555 1555 2.05 LINK OD2 ASP B 220 MG MG B 405 1555 1555 2.04 LINK MG MG B 405 O HOH B 504 1555 1555 2.09 LINK MG MG B 405 O HOH B 545 1555 1555 2.05 LINK MG MG B 405 O HOH B 639 1555 1555 1.97 LINK MG MG B 405 O HOH B 656 1555 1555 2.04 LINK MG MG B 405 O HOH B 704 1555 1555 2.07 SITE 1 AC1 25 ASP A 137 VAL A 142 ASP A 143 GLY A 144 SITE 2 AC1 25 THR A 145 GLU A 146 GLN A 174 TRP A 176 SITE 3 AC1 25 ARG A 197 HIS A 215 VAL A 219 ASP A 220 SITE 4 AC1 25 ARG A 232 LEU A 246 PHE A 248 GLN A 261 SITE 5 AC1 25 LEU A 262 MET A 265 MET A 276 THR A 280 SITE 6 AC1 25 CYN A 407 HOH A 504 HOH A 517 HOH A 560 SITE 7 AC1 25 HOH A 596 SITE 1 AC2 9 LEU A 138 SER A 139 GLY A 140 ASN A 184 SITE 2 AC2 9 LYS A 199 HOH A 543 HOH A 564 HOH A 586 SITE 3 AC2 9 HOH A 724 SITE 1 AC3 8 ARG A 131 ASP A 143 GLY A 144 ARG A 232 SITE 2 AC3 8 GLN A 233 SER A 234 CYN A 407 HOH A 661 SITE 1 AC4 8 GLU A 156 VAL A 157 LYS A 229 CYS A 252 SITE 2 AC4 8 ASN A 257 HOH A 648 ASP B 224 LYS B 226 SITE 1 AC5 7 GLU A 126 ILE A 127 HIS A 128 GLY A 238 SITE 2 AC5 7 HOH A 512 HOH A 597 HOH A 669 SITE 1 AC6 6 ASP A 220 HOH A 504 HOH A 517 HOH A 610 SITE 2 AC6 6 HOH A 689 HOH A 764 SITE 1 AC7 5 ASP A 143 ARG A 232 PHE A 248 HEM A 401 SITE 2 AC7 5 GOL A 403 SITE 1 AC8 25 ASP B 137 VAL B 142 ASP B 143 GLY B 144 SITE 2 AC8 25 THR B 145 GLU B 146 GLN B 174 TRP B 176 SITE 3 AC8 25 ARG B 197 HIS B 215 VAL B 219 ASP B 220 SITE 4 AC8 25 ARG B 232 LEU B 246 PHE B 248 GLN B 261 SITE 5 AC8 25 LEU B 262 MET B 265 MET B 276 THR B 280 SITE 6 AC8 25 CYN B 406 HOH B 504 HOH B 527 HOH B 545 SITE 7 AC8 25 HOH B 561 SITE 1 AC9 8 ARG B 131 ASP B 143 GLY B 144 ARG B 232 SITE 2 AC9 8 GLN B 233 SER B 234 CYN B 406 HOH B 509 SITE 1 AD1 8 ASP A 224 LYS A 226 GLU B 156 VAL B 157 SITE 2 AD1 8 LYS B 229 CYS B 252 ASN B 257 HOH B 583 SITE 1 AD2 8 THR A 239 GLU B 126 ILE B 127 HIS B 128 SITE 2 AD2 8 GLY B 238 HOH B 520 HOH B 551 HOH B 554 SITE 1 AD3 6 ASP B 220 HOH B 504 HOH B 545 HOH B 639 SITE 2 AD3 6 HOH B 656 HOH B 704 SITE 1 AD4 5 ASP B 143 ARG B 232 PHE B 248 HEM B 401 SITE 2 AD4 5 GOL B 402 CRYST1 50.570 75.740 75.710 90.00 107.85 90.00 P 1 21 1 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 0.019775 0.000000 0.006368 0.00000 SCALE2 0.000000 0.013203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013876 0.00000