HEADER OXIDOREDUCTASE 24-JAN-18 6FKT TITLE CRYSTAL STRUCTURE OF A DYE-DECOLORIZING PEROXIDASE R232A VARIANT FROM TITLE 2 KLEBSIELLA 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 VARIANT: R232A; SOURCE 5 GENE: YFEX, AGG09_21550, B1727_13990, B8011_07420, BL102_0001560, SOURCE 6 BN49_3985, BVX91_12125, CEO55_07245, CIT28_09840, CP905_14695, SOURCE 7 PMK1_00271, SAMEA3531778_01640, SM57_03027; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 9 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 4 17-JAN-24 6FKT 1 LINK REVDAT 3 03-OCT-18 6FKT 1 JRNL REVDAT 2 15-AUG-18 6FKT 1 JRNL REMARK REVDAT 1 08-AUG-18 6FKT 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. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.327 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 51706 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.963 REMARK 3 FREE R VALUE TEST SET COUNT : 2566 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 75.2837 - 4.8742 0.99 3042 161 0.1972 0.2306 REMARK 3 2 4.8742 - 3.8689 1.00 2819 178 0.1230 0.1310 REMARK 3 3 3.8689 - 3.3798 1.00 2800 145 0.1413 0.1861 REMARK 3 4 3.3798 - 3.0708 1.00 2793 129 0.1519 0.1869 REMARK 3 5 3.0708 - 2.8507 1.00 2766 137 0.1633 0.2296 REMARK 3 6 2.8507 - 2.6826 1.00 2742 137 0.1602 0.1974 REMARK 3 7 2.6826 - 2.5482 1.00 2767 124 0.1545 0.2130 REMARK 3 8 2.5482 - 2.4373 1.00 2727 150 0.1613 0.2451 REMARK 3 9 2.4373 - 2.3435 1.00 2725 134 0.1600 0.2205 REMARK 3 10 2.3435 - 2.2626 1.00 2722 135 0.1677 0.2737 REMARK 3 11 2.2626 - 2.1919 0.99 2686 137 0.1938 0.2451 REMARK 3 12 2.1919 - 2.1292 1.00 2705 132 0.1857 0.2291 REMARK 3 13 2.1292 - 2.0731 1.00 2689 137 0.1906 0.2385 REMARK 3 14 2.0731 - 2.0226 0.99 2671 153 0.1935 0.2295 REMARK 3 15 2.0226 - 1.9766 0.99 2674 132 0.2065 0.2456 REMARK 3 16 1.9766 - 1.9345 0.98 2630 161 0.2379 0.2733 REMARK 3 17 1.9345 - 1.8958 0.97 2584 153 0.3058 0.3559 REMARK 3 18 1.8958 - 1.8600 0.97 2598 131 0.2847 0.3126 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) : 0.217 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.65 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 : 0.004 4838 REMARK 3 ANGLE : 0.731 6570 REMARK 3 CHIRALITY : 0.044 686 REMARK 3 PLANARITY : 0.003 866 REMARK 3 DIHEDRAL : 10.286 2828 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.7948 23.8384 17.3385 REMARK 3 T TENSOR REMARK 3 T11: 0.1943 T22: 0.1941 REMARK 3 T33: 0.2245 T12: -0.0137 REMARK 3 T13: -0.0076 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.4830 L22: 0.4713 REMARK 3 L33: 0.7491 L12: -0.1122 REMARK 3 L13: 0.0249 L23: 0.1386 REMARK 3 S TENSOR REMARK 3 S11: -0.0093 S12: -0.0479 S13: 0.0060 REMARK 3 S21: 0.0277 S22: 0.0083 S23: 0.0134 REMARK 3 S31: 0.0720 S32: -0.0851 S33: 0.0006 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 6FKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-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 : ESRF REMARK 200 BEAMLINE : MASSIF-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.996 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51833 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 75.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.11340 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 1.70100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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: 6FKS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 29% W/V PEG 3350, 0.15 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 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 165.21333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 82.60667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 123.91000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 41.30333 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 206.51667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 165.21333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 82.60667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 41.30333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 123.91000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 206.51667 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: 4460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 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 799 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 670 LIES ON A SPECIAL POSITION. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLU A 156 HZ1 LYS A 161 1.53 REMARK 500 OE1 GLU B 223 HH TYR B 256 1.54 REMARK 500 O HOH B 678 O HOH B 722 2.16 REMARK 500 O HOH B 516 O HOH B 620 2.16 REMARK 500 O HOH A 692 O HOH A 749 2.17 REMARK 500 O ASN A 147 O HOH A 601 2.18 REMARK 500 OD2 ASP B 224 O HOH B 501 2.18 REMARK 500 O GLU B 204 O HOH B 502 2.19 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 693 O HOH A 693 8555 1.85 REMARK 500 O HOH A 825 O HOH A 825 8555 2.17 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 VAL A 81 135.73 76.67 REMARK 500 SER A 100 -175.38 -172.65 REMARK 500 THR A 269 -102.97 -102.66 REMARK 500 SER B 100 -174.71 -173.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 845 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 846 DISTANCE = 6.41 ANGSTROMS REMARK 525 HOH B 738 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH B 739 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH B 740 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH B 741 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH B 742 DISTANCE = 7.08 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 500 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 215 NE2 REMARK 620 2 HEM A 500 NA 101.4 REMARK 620 3 HEM A 500 NB 89.7 90.4 REMARK 620 4 HEM A 500 NC 89.5 169.0 88.8 REMARK 620 5 HEM A 500 ND 100.1 88.1 170.2 90.8 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 99.6 REMARK 620 3 HEM B 401 NB 88.7 92.1 REMARK 620 4 HEM B 401 NC 89.6 170.8 89.0 REMARK 620 5 HEM B 401 ND 99.0 88.9 172.0 88.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 224 OD2 REMARK 620 2 HOH B 515 O 100.6 REMARK 620 3 HOH B 603 O 89.6 169.1 REMARK 620 4 HOH B 637 O 91.4 88.0 88.0 REMARK 620 5 HOH B 642 O 96.1 85.8 96.9 171.0 REMARK 620 6 HOH B 716 O 173.6 84.2 85.4 84.4 88.4 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FKS RELATED DB: PDB REMARK 900 6FKS CONTAINS THE WILD-TYPE STRUCTURE OF THIS PROTEIN REMARK 900 RELATED ID: 6FIY RELATED DB: PDB REMARK 900 6FIY CONTAINS THE D143A/R232A VARIANT OF THIS STRUCTURE DBREF1 6FKT A 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6FKT A A0A0W8ATM9 1 299 DBREF1 6FKT B 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6FKT B A0A0W8ATM9 1 299 SEQADV 6FKT PRO A -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKT LEU A -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKT GLY A 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKT ALA A 232 UNP A0A0W8ATM ARG 232 CONFLICT SEQADV 6FKT GLY A 300 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKT PRO B -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKT LEU B -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKT GLY B 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FKT ALA B 232 UNP A0A0W8ATM ARG 232 CONFLICT SEQADV 6FKT 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 ALA 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 ALA 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 500 73 HET HEM B 401 73 HET MG B 402 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM MG MAGNESIUM ION HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 5 MG MG 2+ FORMUL 6 HOH *488(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 SER B 68 1 9 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 MET B 186 1 8 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 ALA 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 99 N GLY B 54 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 LYS B 124 N GLU B 20 SHEET 1 AA6 4 VAL B 231 ALA 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 500 1555 1555 2.29 LINK NE2 HIS B 215 FE HEM B 401 1555 1555 2.29 LINK OD2 ASP B 224 MG MG B 402 1555 1555 2.00 LINK MG MG B 402 O HOH B 515 1555 1555 1.99 LINK MG MG B 402 O HOH B 603 1555 1555 2.00 LINK MG MG B 402 O HOH B 637 1555 1555 2.06 LINK MG MG B 402 O HOH B 642 1555 1555 1.94 LINK MG MG B 402 O HOH B 716 1555 1555 2.14 CISPEP 1 ASN A 147 PRO A 148 0 -0.76 CISPEP 2 ASN B 147 PRO B 148 0 1.06 SITE 1 AC1 16 ASP A 137 VAL A 142 GLN A 174 TRP A 176 SITE 2 AC1 16 HIS A 178 ARG A 197 HIS A 215 LEU A 216 SITE 3 AC1 16 VAL A 219 LEU A 246 PHE A 248 GLN A 261 SITE 4 AC1 16 MET A 265 MET A 276 HOH A 632 HOH A 743 SITE 1 AC2 17 VAL B 142 GLN B 174 TRP B 176 HIS B 178 SITE 2 AC2 17 ARG B 197 HIS B 215 LEU B 216 VAL B 219 SITE 3 AC2 17 LEU B 246 PHE B 248 GLN B 261 LEU B 262 SITE 4 AC2 17 MET B 276 HOH B 503 HOH B 506 HOH B 508 SITE 5 AC2 17 HOH B 559 SITE 1 AC3 6 ASP B 224 HOH B 515 HOH B 603 HOH B 637 SITE 2 AC3 6 HOH B 642 HOH B 716 CRYST1 91.160 91.160 247.820 90.00 90.00 120.00 P 65 2 2 24 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 0.010970 0.006333 0.000000 0.00000 SCALE2 0.000000 0.012667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004035 0.00000