HEADER OXIDOREDUCTASE 24-JAN-18 6FKS TITLE CRYSTAL STRUCTURE OF A DYE-DECOLORIZING PEROXIDASE FROM KLEBSIELLA TITLE 2 PNEUMONIAE (KPDYP) 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 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS ALPHA-BETA BARREL, HEME BINDING, DYP, ENZYMATIC REDOX REACTION, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.PFANZAGL,S.HOFBAUER,G.MLYNEK REVDAT 5 17-JAN-24 6FKS 1 LINK REVDAT 4 02-OCT-19 6FKS 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQADV SEQRES LINK SITE REVDAT 4 3 1 CRYST1 ATOM REVDAT 3 03-OCT-18 6FKS 1 JRNL REVDAT 2 15-AUG-18 6FKS 1 JRNL REVDAT 1 08-AUG-18 6FKS 0 JRNL AUTH V.PFANZAGL,K.NYS,M.BELLEI,H.MICHLITS,G.MLYNEK,G.BATTISTUZZI, JRNL AUTH 2 K.DJINOVIC-CARUGO,S.VAN DOORSLAER,P.G.FURTMULLER,S.HOFBAUER, JRNL AUTH 3 C.OBINGER JRNL TITL ROLES OF DISTAL ASPARTATE AND ARGININE OF B-CLASS JRNL TITL 2 DYE-DECOLORIZING PEROXIDASE IN HETEROLYTIC HYDROGEN PEROXIDE JRNL TITL 3 CLEAVAGE. JRNL REF J. BIOL. CHEM. V. 293 14823 2018 JRNL REFN ESSN 1083-351X JRNL PMID 30072383 JRNL DOI 10.1074/JBC.RA118.004773 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.348 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 69396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.925 REMARK 3 FREE R VALUE TEST SET COUNT : 3418 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 52.2455 - 4.6142 0.97 2855 138 0.1902 0.1893 REMARK 3 2 4.6142 - 3.6627 0.97 2795 140 0.1200 0.1375 REMARK 3 3 3.6627 - 3.1998 0.98 2792 148 0.1245 0.1422 REMARK 3 4 3.1998 - 2.9073 0.97 2769 155 0.1243 0.1670 REMARK 3 5 2.9073 - 2.6989 0.97 2752 157 0.1223 0.1587 REMARK 3 6 2.6989 - 2.5398 0.98 2783 153 0.1163 0.1654 REMARK 3 7 2.5398 - 2.4126 0.98 2809 113 0.1155 0.1918 REMARK 3 8 2.4126 - 2.3076 0.98 2790 152 0.1056 0.1405 REMARK 3 9 2.3076 - 2.2187 0.97 2735 168 0.1025 0.1485 REMARK 3 10 2.2187 - 2.1422 0.97 2747 141 0.1050 0.1567 REMARK 3 11 2.1422 - 2.0752 0.98 2777 138 0.1027 0.1624 REMARK 3 12 2.0752 - 2.0159 0.99 2761 163 0.0994 0.1686 REMARK 3 13 2.0159 - 1.9628 0.98 2791 143 0.1002 0.1780 REMARK 3 14 1.9628 - 1.9149 0.97 2750 144 0.1043 0.1487 REMARK 3 15 1.9149 - 1.8714 0.99 2782 131 0.1172 0.1873 REMARK 3 16 1.8714 - 1.8315 0.95 2708 129 0.1229 0.1831 REMARK 3 17 1.8315 - 1.7949 0.96 2751 117 0.1277 0.1902 REMARK 3 18 1.7949 - 1.7610 0.97 2721 140 0.1327 0.1726 REMARK 3 19 1.7610 - 1.7296 0.97 2736 142 0.1351 0.2109 REMARK 3 20 1.7296 - 1.7003 0.97 2766 126 0.1433 0.2256 REMARK 3 21 1.7003 - 1.6728 0.96 2706 150 0.1588 0.2333 REMARK 3 22 1.6728 - 1.6471 0.96 2690 156 0.1638 0.2617 REMARK 3 23 1.6471 - 1.6229 0.96 2689 151 0.1791 0.2164 REMARK 3 24 1.6229 - 1.6000 0.89 2523 123 0.1785 0.2123 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.141 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 4908 REMARK 3 ANGLE : 0.967 6663 REMARK 3 CHIRALITY : 0.105 692 REMARK 3 PLANARITY : 0.005 878 REMARK 3 DIHEDRAL : 13.103 2874 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008419. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-17 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 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 : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69426 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 52.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.04149 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.44570 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.210 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: 5DE0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 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 280 298.15K 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 37.92500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 GLY A 300 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 HH12 ARG A 254 O HOH A 503 1.58 REMARK 500 HZ3 LYS B 35 OXT GLY B 300 1.58 REMARK 500 O HOH A 698 O HOH A 724 1.87 REMARK 500 O HOH A 501 O HOH A 733 1.95 REMARK 500 O HOH B 511 O HOH B 713 2.02 REMARK 500 O HOH B 536 O HOH B 722 2.02 REMARK 500 O HOH A 585 O HOH A 739 2.03 REMARK 500 O HOH B 509 O HOH B 525 2.04 REMARK 500 NH2 ARG B 102 O HOH B 501 2.05 REMARK 500 O HOH B 629 O HOH B 665 2.06 REMARK 500 O HOH A 560 O HOH A 741 2.07 REMARK 500 O HOH A 745 O HOH A 754 2.08 REMARK 500 O HOH B 701 O HOH B 715 2.10 REMARK 500 O HOH A 659 O HOH A 720 2.15 REMARK 500 OE1 GLN B 260 O HOH B 502 2.17 REMARK 500 O HOH B 611 O HOH B 667 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 543 O HOH A 741 2249 1.91 REMARK 500 O HOH B 616 O HOH B 718 22510 1.98 REMARK 500 O HOH A 706 O HOH A 726 2159 2.07 REMARK 500 O HOH A 733 O HOH A 752 2259 2.17 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 VAL B 171 CG1 - CB - CG2 ANGL. DEV. = 12.6 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 -177.18 -174.08 REMARK 500 SER B 100 -174.31 -173.09 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 97.5 REMARK 620 3 HEM A 401 NB 93.0 89.8 REMARK 620 4 HEM A 401 NC 93.0 169.4 88.5 REMARK 620 5 HEM A 401 ND 98.8 89.3 168.2 90.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD2 REMARK 620 2 HOH A 529 O 91.6 REMARK 620 3 HOH A 546 O 90.1 87.6 REMARK 620 4 HOH A 649 O 83.0 87.2 171.3 REMARK 620 5 HOH A 662 O 86.2 177.4 93.8 91.1 REMARK 620 6 HOH A 751 O 172.3 90.3 97.4 89.7 91.7 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 97.3 REMARK 620 3 HEM B 401 NB 93.3 88.4 REMARK 620 4 HEM B 401 NC 93.2 169.2 88.7 REMARK 620 5 HEM B 401 ND 98.3 92.6 168.1 88.1 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 510 O 85.7 REMARK 620 3 HOH B 523 O 90.3 93.0 REMARK 620 4 HOH B 562 O 89.1 173.3 91.2 REMARK 620 5 HOH B 631 O 95.3 92.2 172.6 84.1 REMARK 620 6 HOH B 709 O 174.5 91.8 84.9 93.7 89.7 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 MG A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FIY RELATED DB: PDB REMARK 900 6FIY CONTAINS THE D143A/R232A VARIANT OF THIS PROTEIN DBREF1 6FKS A 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6FKS A A0A0W8ATM9 1 299 DBREF1 6FKS B 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6FKS B A0A0W8ATM9 1 299 SEQADV 6FKS PRO A -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKS LEU A -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKS GLY A 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKS GLY A 300 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKS PRO B -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKS LEU B -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKS GLY B 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKS 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 MG A 405 1 HET HEM B 401 73 HET GOL B 402 14 HET MG B 403 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 7 MG 2(MG 2+) FORMUL 11 HOH *525(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 ASP B 206 ARG B 210 5 5 HELIX 24 AC6 SER B 214 ASP B 220 1 7 HELIX 25 AC7 ARG B 254 PHE B 266 1 13 HELIX 26 AC8 ASP B 274 ARG B 278 5 5 HELIX 27 AC9 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 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 HEM A 401 1555 1555 2.17 LINK OD2 ASP A 220 MG MG A 405 1555 1555 2.23 LINK MG MG A 405 O HOH A 529 1555 1555 2.02 LINK MG MG A 405 O HOH A 546 1555 1555 2.00 LINK MG MG A 405 O HOH A 649 1555 1555 2.08 LINK MG MG A 405 O HOH A 662 1555 1555 2.00 LINK MG MG A 405 O HOH A 751 1555 1555 1.95 LINK NE2 HIS B 215 FE HEM B 401 1555 1555 2.21 LINK OD2 ASP B 220 MG MG B 403 1555 1555 2.10 LINK MG MG B 403 O HOH B 510 1555 1555 2.00 LINK MG MG B 403 O HOH B 523 1555 1555 2.14 LINK MG MG B 403 O HOH B 562 1555 1555 1.89 LINK MG MG B 403 O HOH B 631 1555 1555 2.09 LINK MG MG B 403 O HOH B 709 1555 1555 2.07 SITE 1 AC1 24 ASP A 137 VAL A 142 ASP A 143 GLY A 144 SITE 2 AC1 24 THR A 145 GLU A 146 GLN A 174 TRP A 176 SITE 3 AC1 24 HIS A 178 ARG A 197 HIS A 215 VAL A 219 SITE 4 AC1 24 ASP A 220 ARG A 232 LEU A 246 PHE A 248 SITE 5 AC1 24 GLN A 261 MET A 265 MET A 276 THR A 280 SITE 6 AC1 24 HOH A 529 HOH A 538 HOH A 546 HOH A 573 SITE 1 AC2 6 LEU A 138 SER A 139 ASN A 184 LYS A 199 SITE 2 AC2 6 HOH A 505 HOH A 557 SITE 1 AC3 10 ARG A 131 ASP A 143 ASN A 147 ARG A 232 SITE 2 AC3 10 GLN A 233 SER A 234 HOH A 508 HOH A 526 SITE 3 AC3 10 HOH A 592 HOH A 680 SITE 1 AC4 8 GLU A 156 VAL A 157 CYS A 252 ARG A 254 SITE 2 AC4 8 ASN A 257 HOH A 689 HOH A 698 ASP B 224 SITE 1 AC5 6 ASP A 220 HOH A 529 HOH A 546 HOH A 649 SITE 2 AC5 6 HOH A 662 HOH A 751 SITE 1 AC6 23 ASP B 137 VAL B 142 ASP B 143 GLY B 144 SITE 2 AC6 23 THR B 145 GLU B 146 GLN B 174 TRP B 176 SITE 3 AC6 23 HIS B 178 ARG B 197 HIS B 215 VAL B 219 SITE 4 AC6 23 ASP B 220 ARG B 232 LEU B 246 PHE B 248 SITE 5 AC6 23 GLN B 261 MET B 265 MET B 276 HOH B 523 SITE 6 AC6 23 HOH B 562 HOH B 567 HOH B 620 SITE 1 AC7 10 ARG B 131 ASP B 143 ASN B 147 ARG B 232 SITE 2 AC7 10 GLN B 233 SER B 234 HOH B 504 HOH B 570 SITE 3 AC7 10 HOH B 625 HOH B 655 SITE 1 AC8 6 ASP B 220 HOH B 510 HOH B 523 HOH B 562 SITE 2 AC8 6 HOH B 631 HOH B 709 CRYST1 50.520 75.850 75.640 90.00 107.86 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 0.019794 0.000000 0.006378 0.00000 SCALE2 0.000000 0.013184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013890 0.00000