HEADER OXIDOREDUCTASE 19-JAN-18 6FIY TITLE CRYSTAL STRUCTURE OF A DYE-DECOLORIZING PEROXIDASE D143AR232A VARIANT TITLE 2 FROM 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: D143AR232A; 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(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008 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 6FIY 1 LINK REVDAT 4 06-NOV-19 6FIY 1 REMARK REVDAT 3 03-OCT-18 6FIY 1 JRNL REVDAT 2 15-AUG-18 6FIY 1 JRNL REVDAT 1 08-AUG-18 6FIY 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. 1.09 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.344 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 224598 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.125 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.998 REMARK 3 FREE R VALUE TEST SET COUNT : 11226 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 52.5282 - 3.3866 0.98 7256 367 0.1346 0.1551 REMARK 3 2 3.3866 - 2.6881 0.98 7132 350 0.1235 0.1403 REMARK 3 3 2.6881 - 2.3483 0.98 7098 400 0.1083 0.1274 REMARK 3 4 2.3483 - 2.1336 0.98 7089 401 0.0975 0.1144 REMARK 3 5 2.1336 - 1.9806 0.98 7131 361 0.0945 0.1153 REMARK 3 6 1.9806 - 1.8639 0.99 7134 407 0.0921 0.1181 REMARK 3 7 1.8639 - 1.7705 0.99 7186 384 0.0882 0.1190 REMARK 3 8 1.7705 - 1.6934 1.00 7183 363 0.0938 0.1305 REMARK 3 9 1.6934 - 1.6282 1.00 7196 399 0.0944 0.1220 REMARK 3 10 1.6282 - 1.5720 0.95 6864 361 0.0920 0.1332 REMARK 3 11 1.5720 - 1.5229 0.97 7039 339 0.0940 0.1371 REMARK 3 12 1.5229 - 1.4794 0.99 7207 357 0.1019 0.1411 REMARK 3 13 1.4794 - 1.4404 0.99 7170 342 0.1045 0.1368 REMARK 3 14 1.4404 - 1.4053 1.00 7138 410 0.1133 0.1543 REMARK 3 15 1.4053 - 1.3733 1.00 7224 389 0.1254 0.1642 REMARK 3 16 1.3733 - 1.3441 1.00 7192 387 0.1379 0.1787 REMARK 3 17 1.3441 - 1.3172 1.00 7215 399 0.1418 0.1684 REMARK 3 18 1.3172 - 1.2923 1.00 7134 395 0.1478 0.1692 REMARK 3 19 1.2923 - 1.2693 1.00 7105 393 0.1555 0.1875 REMARK 3 20 1.2693 - 1.2477 0.99 7147 384 0.1639 0.1964 REMARK 3 21 1.2477 - 1.2276 0.99 7240 350 0.1687 0.1917 REMARK 3 22 1.2276 - 1.2087 0.96 6945 318 0.1798 0.2100 REMARK 3 23 1.2087 - 1.1909 0.95 6901 333 0.1922 0.2352 REMARK 3 24 1.1909 - 1.1742 0.97 6996 365 0.2041 0.2261 REMARK 3 25 1.1742 - 1.1583 0.98 7045 401 0.2121 0.2451 REMARK 3 26 1.1583 - 1.1433 0.98 7034 376 0.2203 0.2334 REMARK 3 27 1.1433 - 1.1290 0.98 7072 360 0.2256 0.2472 REMARK 3 28 1.1290 - 1.1154 0.99 7117 389 0.2357 0.2393 REMARK 3 29 1.1154 - 1.1024 0.98 7021 389 0.2535 0.2823 REMARK 3 30 1.1024 - 1.0900 0.99 7161 357 0.2725 0.3110 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.825 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.15 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 5170 REMARK 3 ANGLE : 1.113 7054 REMARK 3 CHIRALITY : 0.085 736 REMARK 3 PLANARITY : 0.008 940 REMARK 3 DIHEDRAL : 14.648 1895 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 6FIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1200008396. 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) : 0.966 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 : 224631 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 52.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.04589 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.69100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.280 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 (%): 41.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 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 280 293.15K 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 38.15500 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: 5790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 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 HZ3 LYS A 226 O HOH A 501 1.40 REMARK 500 HZ1 LYS B 226 O HOH B 508 1.45 REMARK 500 HE22 GLN B 297 O HOH B 502 1.48 REMARK 500 HZ3 LYS B 222 O HOH B 514 1.53 REMARK 500 HZ3 LYS A 229 O HOH A 504 1.55 REMARK 500 HZ3 LYS A 272 O HOH A 505 1.57 REMARK 500 O HOH B 689 O HOH B 700 1.84 REMARK 500 O HOH A 556 O HOH A 820 1.86 REMARK 500 O HOH B 632 O HOH B 856 1.91 REMARK 500 O HOH A 765 O HOH A 773 1.92 REMARK 500 O HOH A 504 O HOH A 542 1.93 REMARK 500 O HOH B 820 O HOH B 891 1.96 REMARK 500 O HOH B 828 O HOH B 890 2.03 REMARK 500 O HOH B 717 O HOH B 783 2.04 REMARK 500 O HOH A 757 O HOH A 766 2.05 REMARK 500 O HOH A 691 O HOH A 820 2.07 REMARK 500 O HOH A 697 O HOH A 837 2.07 REMARK 500 O HOH B 561 O HOH B 678 2.07 REMARK 500 O HOH A 738 O HOH A 823 2.08 REMARK 500 O HOH B 694 O HOH B 857 2.09 REMARK 500 O HOH A 723 O HOH A 787 2.10 REMARK 500 O LYS B 24 O HOH B 501 2.10 REMARK 500 O HOH A 665 O HOH A 777 2.10 REMARK 500 O HOH A 699 O HOH A 809 2.10 REMARK 500 O HOH A 511 O HOH A 829 2.11 REMARK 500 O HOH A 670 O HOH A 820 2.13 REMARK 500 O HOH A 794 O HOH A 801 2.14 REMARK 500 O HOH A 773 O HOH A 866 2.14 REMARK 500 O HOH A 677 O HOH A 752 2.16 REMARK 500 O HOH B 532 O HOH B 578 2.16 REMARK 500 O HOH A 865 O HOH A 869 2.17 REMARK 500 O HOH A 641 O HOH A 646 2.17 REMARK 500 O HOH B 580 O HOH B 856 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 505 O HOH A 772 2655 2.01 REMARK 500 O HOH A 792 O HOH A 868 2545 2.08 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. = -3.9 DEGREES REMARK 500 ARG B 278 NE - CZ - NH2 ANGL. DEV. = -3.6 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 -174.80 -173.03 REMARK 500 ASP A 224 53.81 38.29 REMARK 500 SER B 100 -175.65 -171.76 REMARK 500 PHE B 279 -11.66 -142.34 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 871 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH B 905 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH B 906 DISTANCE = 7.81 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 92.5 REMARK 620 3 HEM A 401 NB 92.6 89.7 REMARK 620 4 HEM A 401 NC 94.1 173.5 90.0 REMARK 620 5 HEM A 401 ND 97.0 89.1 170.4 90.1 REMARK 620 6 HOH A 665 O 175.5 83.0 87.6 90.5 82.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 220 OD2 REMARK 620 2 HOH A 516 O 93.7 REMARK 620 3 HOH A 520 O 86.5 93.8 REMARK 620 4 HOH A 553 O 89.0 88.1 175.2 REMARK 620 5 HOH A 747 O 89.2 175.0 90.5 87.8 REMARK 620 6 HOH A 804 O 174.1 86.2 87.6 96.9 91.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 215 NE2 REMARK 620 2 HEM B 401 NA 91.9 REMARK 620 3 HEM B 401 NB 92.7 89.6 REMARK 620 4 HEM B 401 NC 93.5 174.5 90.1 REMARK 620 5 HEM B 401 ND 95.1 89.5 172.2 90.1 REMARK 620 6 HOH B 672 O 175.2 83.4 88.7 91.1 83.6 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 514 O 85.4 REMARK 620 3 HOH B 520 O 91.9 91.9 REMARK 620 4 HOH B 576 O 87.9 172.5 85.0 REMARK 620 5 HOH B 742 O 89.5 94.0 174.0 89.3 REMARK 620 6 HOH B 830 O 175.6 90.3 87.3 96.3 91.7 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 MG 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 GOL B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 404 DBREF1 6FIY A 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6FIY A A0A0W8ATM9 1 299 DBREF1 6FIY B 1 299 UNP A0A0W8ATM9_KLEPN DBREF2 6FIY B A0A0W8ATM9 1 299 SEQADV 6FIY PRO A -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FIY LEU A -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FIY GLY A 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FIY ALA A 143 UNP A0A0W8ATM ASP 143 CONFLICT SEQADV 6FIY ALA A 232 UNP A0A0W8ATM ARG 232 CONFLICT SEQADV 6FIY GLY A 300 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FIY PRO B -2 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FIY LEU B -1 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FIY GLY B 0 UNP A0A0W8ATM EXPRESSION TAG SEQADV 6FIY ALA B 143 UNP A0A0W8ATM ASP 143 CONFLICT SEQADV 6FIY ALA B 232 UNP A0A0W8ATM ARG 232 CONFLICT SEQADV 6FIY 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 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 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 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 401 73 HET GOL A 402 14 HET GOL A 403 14 HET MG A 404 1 HET HEM B 401 73 HET GOL B 402 14 HET GOL B 403 14 HET MG B 404 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 6 MG 2(MG 2+) FORMUL 11 HOH *777(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 19 O ILE A 96 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 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 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 401 1555 1555 2.08 LINK OD2 ASP A 220 MG MG A 404 1555 1555 2.17 LINK FE HEM A 401 O HOH A 665 1555 1555 2.19 LINK MG MG A 404 O HOH A 516 1555 1555 2.06 LINK MG MG A 404 O HOH A 520 1555 1555 1.91 LINK MG MG A 404 O HOH A 553 1555 1555 2.01 LINK MG MG A 404 O HOH A 747 1555 1555 2.08 LINK MG MG A 404 O HOH A 804 1555 1555 2.08 LINK NE2 HIS B 215 FE HEM B 401 1555 1555 2.08 LINK OD2 ASP B 220 MG MG B 404 1555 1555 2.14 LINK FE HEM B 401 O HOH B 672 1555 1555 2.17 LINK MG MG B 404 O HOH B 514 1555 1555 1.98 LINK MG MG B 404 O HOH B 520 1555 1555 2.13 LINK MG MG B 404 O HOH B 576 1555 1555 2.04 LINK MG MG B 404 O HOH B 742 1555 1555 2.02 LINK MG MG B 404 O HOH B 830 1555 1555 1.98 SITE 1 AC1 25 ASP A 137 VAL A 142 GLY A 144 THR A 145 SITE 2 AC1 25 GLU A 146 GLN A 174 TRP A 176 HIS A 178 SITE 3 AC1 25 ARG A 197 HIS A 215 VAL A 219 ASP A 220 SITE 4 AC1 25 LEU A 246 PHE A 248 GLN A 261 MET A 265 SITE 5 AC1 25 MET A 276 THR A 280 GOL A 402 HOH A 516 SITE 6 AC1 25 HOH A 553 HOH A 583 HOH A 654 HOH A 665 SITE 7 AC1 25 HOH A 667 SITE 1 AC2 9 GLY A 144 THR A 145 GLU A 146 ASN A 147 SITE 2 AC2 9 ILE A 230 ALA A 232 HEM A 401 HOH A 659 SITE 3 AC2 9 HOH A 665 SITE 1 AC3 8 GLU A 156 VAL A 157 LYS A 161 CYS A 252 SITE 2 AC3 8 ARG A 254 ASN A 257 ASP B 224 HOH B 906 SITE 1 AC4 6 ASP A 220 HOH A 516 HOH A 520 HOH A 553 SITE 2 AC4 6 HOH A 747 HOH A 804 SITE 1 AC5 25 ASP B 137 VAL B 142 GLY B 144 THR B 145 SITE 2 AC5 25 GLU B 146 GLN B 174 TRP B 176 HIS B 178 SITE 3 AC5 25 ARG B 197 HIS B 215 VAL B 219 ASP B 220 SITE 4 AC5 25 LEU B 246 PHE B 248 GLN B 261 MET B 265 SITE 5 AC5 25 MET B 276 THR B 280 GOL B 402 HOH B 520 SITE 6 AC5 25 HOH B 576 HOH B 589 HOH B 641 HOH B 672 SITE 7 AC5 25 HOH B 686 SITE 1 AC6 7 GLY B 144 ASN B 147 ILE B 230 ALA B 232 SITE 2 AC6 7 HEM B 401 HOH B 672 HOH B 682 SITE 1 AC7 8 ASP A 224 HOH A 502 GLU B 156 VAL B 157 SITE 2 AC7 8 LYS B 161 ASN B 257 HOH B 570 HOH B 702 SITE 1 AC8 6 ASP B 220 HOH B 514 HOH B 520 HOH B 576 SITE 2 AC8 6 HOH B 742 HOH B 830 CRYST1 50.620 76.310 75.940 90.00 107.92 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 0.019755 0.000000 0.006388 0.00000 SCALE2 0.000000 0.013104 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013840 0.00000