HEADER OXIDOREDUCTASE 25-JAN-18 6FL2 TITLE CRYSTAL STRUCTURE OF A DYE-DECOLORIZING PEROXIDASE D143A 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; COMPND 7 MUTATION: 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 4 17-JAN-24 6FL2 1 LINK REVDAT 3 03-OCT-18 6FL2 1 JRNL REVDAT 2 15-AUG-18 6FL2 1 JRNL REVDAT 1 08-AUG-18 6FL2 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. 1.27 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) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.348 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 141989 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.116 REMARK 3 R VALUE (WORKING SET) : 0.114 REMARK 3 FREE R VALUE : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.898 REMARK 3 FREE R VALUE TEST SET COUNT : 6954 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 52.7293 - 3.9457 0.97 4597 227 0.1457 0.1493 REMARK 3 2 3.9457 - 3.1319 0.97 4573 224 0.1209 0.1257 REMARK 3 3 3.1319 - 2.7360 0.96 4479 210 0.1211 0.1437 REMARK 3 4 2.7360 - 2.4859 0.96 4424 251 0.1138 0.1462 REMARK 3 5 2.4859 - 2.3077 0.96 4461 224 0.1085 0.1304 REMARK 3 6 2.3077 - 2.1716 0.96 4523 227 0.1008 0.1252 REMARK 3 7 2.1716 - 2.0629 0.96 4432 242 0.0919 0.1151 REMARK 3 8 2.0629 - 1.9731 0.96 4454 213 0.0881 0.1175 REMARK 3 9 1.9731 - 1.8971 0.96 4454 242 0.0896 0.1109 REMARK 3 10 1.8971 - 1.8316 0.97 4463 250 0.0929 0.1382 REMARK 3 11 1.8316 - 1.7744 0.97 4460 251 0.0915 0.1348 REMARK 3 12 1.7744 - 1.7236 0.97 4524 235 0.0889 0.1264 REMARK 3 13 1.7236 - 1.6783 0.98 4492 251 0.0878 0.1360 REMARK 3 14 1.6783 - 1.6373 0.98 4507 225 0.0874 0.1306 REMARK 3 15 1.6373 - 1.6001 0.98 4561 242 0.0902 0.1400 REMARK 3 16 1.6001 - 1.5660 0.98 4524 224 0.0977 0.1372 REMARK 3 17 1.5660 - 1.5347 0.98 4477 236 0.0972 0.1475 REMARK 3 18 1.5347 - 1.5057 0.98 4518 239 0.1005 0.1402 REMARK 3 19 1.5057 - 1.4789 0.97 4500 223 0.1063 0.1701 REMARK 3 20 1.4789 - 1.4538 0.97 4499 241 0.1078 0.1472 REMARK 3 21 1.4538 - 1.4303 0.98 4522 260 0.1114 0.1519 REMARK 3 22 1.4303 - 1.4083 0.98 4501 226 0.1242 0.1615 REMARK 3 23 1.4083 - 1.3876 0.98 4582 221 0.1315 0.1690 REMARK 3 24 1.3876 - 1.3681 0.98 4491 235 0.1380 0.1691 REMARK 3 25 1.3681 - 1.3496 0.98 4554 239 0.1442 0.2040 REMARK 3 26 1.3496 - 1.3320 0.98 4488 228 0.1490 0.1990 REMARK 3 27 1.3320 - 1.3154 0.97 4493 216 0.1561 0.2020 REMARK 3 28 1.3154 - 1.2995 0.97 4504 220 0.1668 0.2068 REMARK 3 29 1.2995 - 1.2844 0.97 4520 219 0.1842 0.2223 REMARK 3 30 1.2844 - 1.2700 0.97 4458 213 0.1991 0.2602 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) : 0.101 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.792 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.66 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 : 0.010 5003 REMARK 3 ANGLE : 1.075 6805 REMARK 3 CHIRALITY : 0.083 710 REMARK 3 PLANARITY : 0.007 900 REMARK 3 DIHEDRAL : 14.941 1824 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 6FL2 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_1200008510. 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 : NULL 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) : 0.966 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 : 142004 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 REMARK 200 RESOLUTION RANGE LOW (A) : 52.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 1.400 REMARK 200 R MERGE (I) : 0.03012 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42410 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.630 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 (%): 42.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 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 38.34500 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: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 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 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 HE ARG A 254 O HOH A 502 1.48 REMARK 500 HZ3 LYS B 229 O HOH B 504 1.49 REMARK 500 HZ2 LYS A 229 O HOH A 503 1.51 REMARK 500 HE ARG B 254 O HOH B 502 1.52 REMARK 500 HZ2 LYS B 222 O HOH B 505 1.52 REMARK 500 HZ1 LYS A 222 O HOH A 506 1.56 REMARK 500 O HOH A 768 O HOH A 820 1.87 REMARK 500 O HOH B 816 O HOH B 885 1.92 REMARK 500 O HOH B 802 O HOH B 893 1.97 REMARK 500 O HOH A 749 O HOH A 781 2.04 REMARK 500 O HOH B 594 O HOH B 799 2.05 REMARK 500 O HOH B 759 O HOH B 799 2.09 REMARK 500 O LYS B 24 O HOH B 501 2.13 REMARK 500 O HOH B 763 O HOH B 918 2.13 REMARK 500 OE2 GLU A 11 O HOH A 501 2.13 REMARK 500 O HOH B 750 O HOH B 876 2.14 REMARK 500 O HOH B 601 O HOH B 878 2.14 REMARK 500 O HOH A 646 O HOH A 796 2.14 REMARK 500 O HOH B 553 O HOH B 839 2.15 REMARK 500 O HOH B 568 O HOH B 692 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 B 551 O HOH B 803 2454 2.13 REMARK 500 O HOH A 513 O HOH A 524 2555 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 295 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 CYS B 13 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG B 278 NE - CZ - NH2 ANGL. DEV. = -3.2 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 -174.05 -173.41 REMARK 500 SER B 100 -177.22 -171.00 REMARK 500 SER B 100 -177.22 -175.14 REMARK 500 PHE B 279 -11.75 -141.02 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 B 927 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH B 928 DISTANCE = 6.14 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 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 215 NE2 REMARK 620 2 HEM A 401 NA 92.1 REMARK 620 3 HEM A 401 NB 90.7 90.5 REMARK 620 4 HEM A 401 NC 92.3 175.5 89.5 REMARK 620 5 HEM A 401 ND 94.8 89.8 174.4 89.7 REMARK 620 6 NO2 A 403 O2 176.2 84.8 87.1 90.7 87.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD2 REMARK 620 2 HOH A 506 O 83.2 REMARK 620 3 HOH A 518 O 89.3 92.8 REMARK 620 4 HOH A 553 O 89.0 172.2 87.1 REMARK 620 5 HOH A 751 O 91.3 91.4 175.8 88.7 REMARK 620 6 HOH A 784 O 172.5 89.4 91.6 98.4 88.4 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 91.9 REMARK 620 3 HEM B 401 NB 91.0 90.2 REMARK 620 4 HEM B 401 NC 91.9 176.2 90.1 REMARK 620 5 HEM B 401 ND 93.7 88.4 175.2 91.0 REMARK 620 6 NO2 B 405 O2 176.4 85.1 87.0 91.2 88.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 220 OD2 REMARK 620 2 HOH B 505 O 83.5 REMARK 620 3 HOH B 517 O 90.1 92.4 REMARK 620 4 HOH B 592 O 88.8 172.1 86.1 REMARK 620 5 HOH B 741 O 87.3 92.3 174.3 88.8 REMARK 620 6 HOH B 852 O 177.5 94.3 88.7 93.3 94.1 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 MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO2 B 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FKS RELATED DB: PDB REMARK 900 6FKS CONTAINS THE WT STRUCTURE OF THIS PROTEIN REMARK 900 RELATED ID: 6FKT RELATED DB: PDB REMARK 900 6FKT CONTAINS THE R232A VARIANT OF THIS PROTEIN REMARK 900 RELATED ID: 6FIY RELATED DB: PDB REMARK 900 6FIY CONTAINS THE D143A/R232A VARIANT DBREF1 6FL2 A 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6FL2 A A0A0W8ATM9 1 299 DBREF1 6FL2 B 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6FL2 B A0A0W8ATM9 1 299 SEQADV 6FL2 PRO A -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FL2 LEU A -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FL2 GLY A 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FL2 ALA A 143 UNP A0A0W8ATM ASP 143 ENGINEERED MUTATION SEQADV 6FL2 GLY A 300 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FL2 PRO B -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FL2 LEU B -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FL2 GLY B 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FL2 ALA B 143 UNP A0A0W8ATM ASP 143 ENGINEERED MUTATION SEQADV 6FL2 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 ALA 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 ALA 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 MG A 402 1 HET NO2 A 403 3 HET HEM B 401 73 HET GOL B 402 14 HET GOL B 403 14 HET MG B 404 1 HET NO2 B 405 3 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM MG MAGNESIUM ION HETNAM NO2 NITRITE ION HETNAM GOL GLYCEROL HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 MG 2(MG 2+) FORMUL 5 NO2 2(N O2 1-) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 11 HOH *795(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 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 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 2.12 LINK OD2 ASP A 220 MG MG A 402 1555 1555 2.24 LINK FE HEM A 401 O2 NO2 A 403 1555 1555 2.12 LINK MG MG A 402 O HOH A 506 1555 1555 1.93 LINK MG MG A 402 O HOH A 518 1555 1555 1.99 LINK MG MG A 402 O HOH A 553 1555 1555 2.04 LINK MG MG A 402 O HOH A 751 1555 1555 2.04 LINK MG MG A 402 O HOH A 784 1555 1555 2.19 LINK NE2 HIS B 215 FE HEM B 401 1555 1555 2.13 LINK OD2 ASP B 220 MG MG B 404 1555 1555 2.20 LINK FE HEM B 401 O2 NO2 B 405 1555 1555 2.14 LINK MG MG B 404 O HOH B 505 1555 1555 1.96 LINK MG MG B 404 O HOH B 517 1555 1555 2.06 LINK MG MG B 404 O HOH B 592 1555 1555 2.02 LINK MG MG B 404 O HOH B 741 1555 1555 2.06 LINK MG MG B 404 O HOH B 852 1555 1555 1.84 SITE 1 AC1 24 ASP A 137 VAL A 142 GLY A 144 THR A 145 SITE 2 AC1 24 GLU A 146 GLN A 174 TRP A 176 HIS A 178 SITE 3 AC1 24 ARG A 197 HIS A 215 VAL A 219 ASP A 220 SITE 4 AC1 24 ARG A 232 LEU A 246 PHE A 248 GLN A 261 SITE 5 AC1 24 MET A 265 MET A 276 THR A 280 NO2 A 403 SITE 6 AC1 24 HOH A 518 HOH A 553 HOH A 610 HOH A 614 SITE 1 AC2 6 ASP A 220 HOH A 506 HOH A 518 HOH A 553 SITE 2 AC2 6 HOH A 751 HOH A 784 SITE 1 AC3 6 ARG A 232 SER A 234 LEU A 246 PHE A 248 SITE 2 AC3 6 HEM A 401 HOH A 566 SITE 1 AC4 24 ASP B 137 VAL B 142 GLY B 144 THR B 145 SITE 2 AC4 24 GLU B 146 GLN B 174 TRP B 176 HIS B 178 SITE 3 AC4 24 ARG B 197 HIS B 215 VAL B 219 ASP B 220 SITE 4 AC4 24 ARG B 232 LEU B 246 PHE B 248 GLN B 261 SITE 5 AC4 24 MET B 265 MET B 276 THR B 280 NO2 B 405 SITE 6 AC4 24 HOH B 517 HOH B 592 HOH B 595 HOH B 622 SITE 1 AC5 8 GLU A 156 VAL A 157 LYS A 161 CYS A 252 SITE 2 AC5 8 ASN A 257 ASP B 224 HOH B 542 HOH B 647 SITE 1 AC6 10 ASP A 224 HOH A 529 GLU B 156 VAL B 157 SITE 2 AC6 10 LYS B 161 CYS B 252 ARG B 254 ASN B 257 SITE 3 AC6 10 HOH B 580 HOH B 693 SITE 1 AC7 6 ASP B 220 HOH B 505 HOH B 517 HOH B 592 SITE 2 AC7 6 HOH B 741 HOH B 852 SITE 1 AC8 6 ARG B 232 SER B 234 LEU B 246 PHE B 248 SITE 2 AC8 6 HEM B 401 HOH B 586 CRYST1 50.760 76.690 76.140 90.00 107.79 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 0.019701 0.000000 0.006321 0.00000 SCALE2 0.000000 0.013040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013793 0.00000