HEADER OXIDOREDUCTASE 14-MAY-19 6RPE TITLE STRUCTURE OF 5% REDUCED 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 6RPE 1 REMARK REVDAT 2 07-OCT-20 6RPE 1 JRNL REVDAT 1 02-SEP-20 6RPE 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.31 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 51216 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 2472 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.72 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1025 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2849 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 982 REMARK 3 BIN R VALUE (WORKING SET) : 0.2802 REMARK 3 BIN FREE R VALUE : 0.3913 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.20 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 : 104 REMARK 3 SOLVENT ATOMS : 785 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.02270 REMARK 3 B22 (A**2) : -2.40110 REMARK 3 B33 (A**2) : 1.37840 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.83540 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.210 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.158 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.126 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.262 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.120 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 : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 10112 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 18263 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2187 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 1726 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 10112 ; 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 : 618 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : 10 ; 1.000 ; HARMONIC REMARK 3 UTILITY ANGLES : 10 ; 1.000 ; HARMONIC REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 11861 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 BOND ANGLES (DEGREES) : 1.15 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.07 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.25 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): 13.9728 1.4360 -2.1255 REMARK 3 T TENSOR REMARK 3 T11: -0.0657 T22: -0.0415 REMARK 3 T33: -0.0577 T12: 0.0037 REMARK 3 T13: -0.0042 T23: 0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.7665 L22: 0.5654 REMARK 3 L33: 0.4082 L12: 0.2262 REMARK 3 L13: 0.1441 L23: -0.0345 REMARK 3 S TENSOR REMARK 3 S11: 0.0180 S12: 0.0474 S13: 0.0256 REMARK 3 S21: -0.0413 S22: -0.0198 S23: 0.0274 REMARK 3 S31: 0.0371 S32: 0.0374 S33: 0.0019 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 25.0908 -0.0183 32.4594 REMARK 3 T TENSOR REMARK 3 T11: -0.0455 T22: -0.0190 REMARK 3 T33: -0.0485 T12: 0.0157 REMARK 3 T13: 0.0006 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.5627 L22: 0.2291 REMARK 3 L33: 0.4206 L12: 0.1696 REMARK 3 L13: 0.0773 L23: 0.0993 REMARK 3 S TENSOR REMARK 3 S11: -0.0226 S12: -0.0211 S13: -0.0073 REMARK 3 S21: 0.0247 S22: 0.0025 S23: -0.0127 REMARK 3 S31: 0.0110 S32: 0.0016 S33: 0.0201 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6RPE 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_1292102360. 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51235 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 36.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 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: PHENIX REMARK 200 STARTING MODEL: 6FKS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 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 38.29600 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: 5510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 HG2 GLN B 3 OE1 GLU B 294 1.40 REMARK 500 CG GLN B 3 OE1 GLU B 294 1.91 REMARK 500 FE HEM B 401 C CYN B 404 2.13 REMARK 500 FE HEM A 401 C CYN A 404 2.13 REMARK 500 FE HEM B 401 C CYN B 404 2.14 REMARK 500 FE HEM A 401 C CYN A 404 2.15 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 152 CD GLU A 152 OE1 -0.068 REMARK 500 GLU B 203 CD GLU B 203 OE1 -0.106 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 SER A 2 13.68 REMARK 500 ASP A 143 18.05 REMARK 500 ARG A 278 14.35 REMARK 500 ALA B 51 11.31 REMARK 500 ALA B 51 11.29 REMARK 500 ASP B 143 14.90 REMARK 500 ASP B 143 -10.40 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 89.9 REMARK 620 3 HEM A 401 NB 91.0 89.9 REMARK 620 4 HEM A 401 NC 91.8 178.0 89.0 REMARK 620 5 HEM A 401 ND 92.8 91.0 176.1 90.1 REMARK 620 N 1 2 3 4 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 89.1 REMARK 620 3 HEM A 401 NB 89.7 89.4 REMARK 620 4 HEM A 401 NC 90.9 177.8 88.4 REMARK 620 5 HEM A 401 ND 92.4 91.6 177.6 90.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD2 REMARK 620 2 HOH A 527 O 96.0 REMARK 620 3 HOH A 570 O 88.1 92.4 REMARK 620 4 HOH A 615 O 87.6 84.4 174.3 REMARK 620 5 HOH A 738 O 91.7 172.1 89.4 94.4 REMARK 620 6 HOH A 801 O 178.5 83.7 93.3 91.0 88.5 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 90.4 REMARK 620 3 HEM B 401 NB 91.5 90.0 REMARK 620 4 HEM B 401 NC 93.0 176.7 89.8 REMARK 620 5 HEM B 401 ND 93.2 90.1 175.3 89.8 REMARK 620 N 1 2 3 4 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 90.0 REMARK 620 3 HEM B 401 NB 90.5 89.6 REMARK 620 4 HEM B 401 NC 92.4 177.3 89.2 REMARK 620 5 HEM B 401 ND 93.3 90.7 176.2 90.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 220 OD2 REMARK 620 2 HOH B 526 O 96.7 REMARK 620 3 HOH B 627 O 88.2 98.6 REMARK 620 4 HOH B 629 O 87.1 94.8 166.3 REMARK 620 5 HOH B 739 O 88.6 171.1 88.7 78.3 REMARK 620 6 HOH B 777 O 174.3 83.9 97.4 87.1 90.2 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 MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CYN B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FKS RELATED DB: PDB REMARK 900 FERROUS FORM OF THE RESTING STATE PROTEIN REMARK 900 RELATED ID: 6RPD RELATED DB: PDB REMARK 900 FERROUS FORM OF THE CYANIDE BOUND PROTEIN DBREF1 6RPE A 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6RPE A A0A0W8ATM9 1 299 DBREF1 6RPE B 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6RPE B A0A0W8ATM9 1 299 SEQADV 6RPE PRO A -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPE LEU A -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPE GLY A 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPE GLY A 300 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPE PRO B -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPE LEU B -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPE GLY B 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6RPE 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 401 146 HET GOL A 402 14 HET MG A 403 1 HET CYN A 404 2 HET HEM B 401 146 HET GOL B 402 14 HET MG B 403 1 HET CYN B 404 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 2(C3 H8 O3) FORMUL 5 MG 2(MG 2+) FORMUL 6 CYN 2(C N 1-) FORMUL 11 HOH *785(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 ALA A 149 VAL A 159 1 11 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 ASP A 206 ARG A 210 5 5 HELIX 11 AB2 SER A 214 ASP A 220 1 7 HELIX 12 AB3 ARG A 254 PHE A 266 1 13 HELIX 13 AB4 ASP A 274 ARG A 278 5 5 HELIX 14 AB5 SER A 292 ALA A 298 1 7 HELIX 15 AB6 ASN B 28 PHE B 48 1 21 HELIX 16 AB7 PRO B 49 LYS B 52 5 4 HELIX 17 AB8 GLY B 60 GLY B 69 1 10 HELIX 18 AB9 TYR B 82 LEU B 86 5 5 HELIX 19 AC1 ARG B 102 GLY B 118 1 17 HELIX 20 AC2 TRP B 132 ARG B 136 5 5 HELIX 21 AC3 GLY B 150 VAL B 159 1 10 HELIX 22 AC4 ASN B 179 ARG B 185 1 7 HELIX 23 AC5 SER B 187 GLY B 196 1 10 HELIX 24 AC6 ASP B 206 ARG B 210 5 5 HELIX 25 AC7 SER B 214 ASP B 220 1 7 HELIX 26 AC8 ARG B 254 PHE B 266 1 13 HELIX 27 AC9 ASP B 274 ARG B 278 5 5 HELIX 28 AD1 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 HIS A 97 N VAL A 56 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 HIS B 97 N VAL B 56 SHEET 3 AA5 4 ALA B 15 LEU B 23 -1 N ILE B 17 O ILE B 98 SHEET 4 AA5 4 ILE B 121 PHE B 130 -1 O LYS B 124 N GLU B 20 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 AHEM A 401 1555 1555 2.08 LINK NE2 HIS A 215 FE BHEM A 401 1555 1555 2.11 LINK OD2 ASP A 220 MG MG A 403 1555 1555 2.08 LINK MG MG A 403 O HOH A 527 1555 1555 2.16 LINK MG MG A 403 O HOH A 570 1555 1555 2.13 LINK MG MG A 403 O HOH A 615 1555 1555 2.05 LINK MG MG A 403 O HOH A 738 1555 1555 2.06 LINK MG MG A 403 O HOH A 801 1555 1555 2.20 LINK NE2 HIS B 215 FE AHEM B 401 1555 1555 2.06 LINK NE2 HIS B 215 FE BHEM B 401 1555 1555 2.08 LINK OD2 ASP B 220 MG MG B 403 1555 1555 2.07 LINK MG MG B 403 O HOH B 526 1555 1555 2.13 LINK MG MG B 403 O HOH B 627 1555 1555 2.00 LINK MG MG B 403 O HOH B 629 1555 1555 2.03 LINK MG MG B 403 O HOH B 739 1555 1555 2.22 LINK MG MG B 403 O HOH B 777 1555 1555 2.11 SITE 1 AC1 26 ASP A 137 VAL A 142 ASP A 143 GLY A 144 SITE 2 AC1 26 THR A 145 GLU A 146 GLN A 174 TRP A 176 SITE 3 AC1 26 HIS A 178 ARG A 197 HIS A 215 VAL A 219 SITE 4 AC1 26 ASP A 220 ARG A 232 LEU A 246 PHE A 248 SITE 5 AC1 26 GLN A 261 LEU A 262 MET A 265 MET A 276 SITE 6 AC1 26 THR A 280 CYN A 404 HOH A 527 HOH A 542 SITE 7 AC1 26 HOH A 570 HOH A 571 SITE 1 AC2 9 GLU A 156 VAL A 157 LYS A 161 CYS A 252 SITE 2 AC2 9 ASN A 257 HOH A 540 HOH A 734 ASP B 224 SITE 3 AC2 9 HOH B 613 SITE 1 AC3 6 ASP A 220 HOH A 527 HOH A 570 HOH A 615 SITE 2 AC3 6 HOH A 738 HOH A 801 SITE 1 AC4 5 ASP A 143 ARG A 232 PHE A 248 HEM A 401 SITE 2 AC4 5 HOH A 525 SITE 1 AC5 26 ASP B 137 VAL B 142 ASP B 143 GLY B 144 SITE 2 AC5 26 THR B 145 GLU B 146 GLN B 174 TRP B 176 SITE 3 AC5 26 HIS B 178 ARG B 197 HIS B 215 VAL B 219 SITE 4 AC5 26 ASP B 220 ARG B 232 LEU B 246 PHE B 248 SITE 5 AC5 26 GLN B 261 LEU B 262 MET B 265 MET B 276 SITE 6 AC5 26 THR B 280 CYN B 404 HOH B 526 HOH B 549 SITE 7 AC5 26 HOH B 627 HOH B 645 SITE 1 AC6 10 ASP A 224 HOH A 514 GLU B 156 VAL B 157 SITE 2 AC6 10 LYS B 161 LYS B 229 CYS B 252 ASN B 257 SITE 3 AC6 10 HOH B 593 HOH B 692 SITE 1 AC7 6 ASP B 220 HOH B 526 HOH B 627 HOH B 629 SITE 2 AC7 6 HOH B 739 HOH B 777 SITE 1 AC8 5 ASP B 143 ARG B 232 PHE B 248 HEM B 401 SITE 2 AC8 5 HOH B 506 CRYST1 50.853 76.592 76.308 90.00 107.87 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 0.019665 0.000000 0.006340 0.00000 SCALE2 0.000000 0.013056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013769 0.00000