HEADER OXIDOREDUCTASE 12-OCT-20 7ANV TITLE MUTATIONAL AND STRUCTURAL ANALYSIS OF AN ANCESTRAL D-TYPE DYE TITLE 2 DECOLORIZING PEROXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANCESTRAL D-TYPE DYE DECOLORIZING PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: GEOTRICHUM CANDIDUM; SOURCE 4 ORGANISM_TAXID: 1173061 KEYWDS DYE DECOLORIZING PEROXIDASE, D-TYPE DYP, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.J.ROZEBOOM,M.W.FRAAIJE REVDAT 4 31-JAN-24 7ANV 1 REMARK REVDAT 3 16-JUN-21 7ANV 1 JRNL REVDAT 2 13-JAN-21 7ANV 1 JRNL REVDAT 1 30-DEC-20 7ANV 0 JRNL AUTH U.A.ZITARE,M.H.HABIB,H.ROZEBOOM,M.L.MASCOTTI,S.TODOROVIC, JRNL AUTH 2 M.W.FRAAIJE JRNL TITL MUTATIONAL AND STRUCTURAL ANALYSIS OF AN ANCESTRAL FUNGAL JRNL TITL 2 DYE-DECOLORIZING PEROXIDASE. JRNL REF FEBS J. V. 288 3602 2021 JRNL REFN ISSN 1742-464X JRNL PMID 33369202 JRNL DOI 10.1111/FEBS.15687 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0266 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 52613 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2715 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2991 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 152 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3616 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 398 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.31000 REMARK 3 B22 (A**2) : -0.89000 REMARK 3 B33 (A**2) : -0.42000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.093 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.669 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3821 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3536 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5205 ; 1.686 ; 1.672 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8176 ; 1.431 ; 1.598 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 469 ; 7.108 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 206 ;33.858 ;23.350 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 600 ;12.173 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;21.812 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 480 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4428 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 867 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 24 A 142 REMARK 3 ORIGIN FOR THE GROUP (A): -2.3210 -2.4580 -8.2750 REMARK 3 T TENSOR REMARK 3 T11: 0.0806 T22: 0.0723 REMARK 3 T33: 0.0068 T12: -0.0164 REMARK 3 T13: -0.0114 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 0.7450 L22: 0.3481 REMARK 3 L33: 1.6427 L12: -0.1112 REMARK 3 L13: -0.2782 L23: 0.2907 REMARK 3 S TENSOR REMARK 3 S11: 0.0012 S12: -0.0790 S13: 0.0039 REMARK 3 S21: 0.0295 S22: 0.0003 S23: 0.0271 REMARK 3 S31: -0.0005 S32: -0.0820 S33: -0.0016 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 143 A 162 REMARK 3 ORIGIN FOR THE GROUP (A): 9.4500 -23.5950 -9.1910 REMARK 3 T TENSOR REMARK 3 T11: 0.6226 T22: 0.1683 REMARK 3 T33: 0.1432 T12: 0.0836 REMARK 3 T13: -0.0896 T23: 0.0865 REMARK 3 L TENSOR REMARK 3 L11: 3.9588 L22: 9.7648 REMARK 3 L33: 12.3067 L12: -1.4169 REMARK 3 L13: 0.5951 L23: 0.9847 REMARK 3 S TENSOR REMARK 3 S11: 0.2517 S12: -0.0738 S13: -0.4843 REMARK 3 S21: 0.6922 S22: 0.3063 S23: 0.5833 REMARK 3 S31: 2.0865 S32: 0.3249 S33: -0.5579 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 163 A 332 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5330 -1.5960 -19.0000 REMARK 3 T TENSOR REMARK 3 T11: 0.0755 T22: 0.0457 REMARK 3 T33: 0.0073 T12: -0.0146 REMARK 3 T13: -0.0141 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 0.3718 L22: 0.1475 REMARK 3 L33: 1.1287 L12: -0.0180 REMARK 3 L13: -0.3093 L23: 0.0122 REMARK 3 S TENSOR REMARK 3 S11: 0.0485 S12: -0.0850 S13: 0.0148 REMARK 3 S21: -0.0019 S22: -0.0055 S23: -0.0158 REMARK 3 S31: -0.0368 S32: 0.1247 S33: -0.0430 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 333 A 383 REMARK 3 ORIGIN FOR THE GROUP (A): 8.7890 -2.3830 -38.5490 REMARK 3 T TENSOR REMARK 3 T11: 0.1365 T22: 0.0699 REMARK 3 T33: 0.0309 T12: 0.0093 REMARK 3 T13: -0.0058 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.2589 L22: 1.2345 REMARK 3 L33: 1.2745 L12: 0.3668 REMARK 3 L13: -0.3418 L23: 0.8135 REMARK 3 S TENSOR REMARK 3 S11: 0.0489 S12: 0.1013 S13: 0.1112 REMARK 3 S21: -0.1538 S22: -0.0416 S23: 0.0934 REMARK 3 S31: -0.1058 S32: -0.0852 S33: -0.0073 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 384 A 511 REMARK 3 ORIGIN FOR THE GROUP (A): 11.1400 -11.1170 -22.8310 REMARK 3 T TENSOR REMARK 3 T11: 0.1007 T22: 0.0472 REMARK 3 T33: 0.0146 T12: 0.0052 REMARK 3 T13: -0.0153 T23: 0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.5522 L22: 0.2232 REMARK 3 L33: 0.9086 L12: -0.0551 REMARK 3 L13: -0.3627 L23: 0.0477 REMARK 3 S TENSOR REMARK 3 S11: -0.0316 S12: -0.0694 S13: -0.0393 REMARK 3 S21: 0.0013 S22: 0.0159 S23: -0.0119 REMARK 3 S31: 0.1305 S32: 0.0811 S33: 0.0157 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 7ANV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292111688. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55396 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 59.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 10.30 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.75900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6FSK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M AMMONIUM SULFATE, 0.1 M MES, PH REMARK 280 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 29.54250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.19500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.55350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.19500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.54250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.55350 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 LYS A 85 REMARK 465 LYS A 86 REMARK 465 SER A 87 REMARK 465 ASN A 88 REMARK 465 GLN A 89 REMARK 465 LYS A 90 REMARK 465 SER A 91 REMARK 465 GLY A 92 REMARK 465 LYS A 93 REMARK 465 PRO A 94 REMARK 465 PRO A 95 REMARK 465 GLU A 96 REMARK 465 LEU A 97 REMARK 465 ASN A 145 REMARK 465 ALA A 146 REMARK 465 GLY A 147 REMARK 465 ALA A 148 REMARK 465 LYS A 149 REMARK 465 ALA A 258 REMARK 465 ASN A 259 REMARK 465 ASN A 260 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 NH1 ARG A 345 OE1 GLU A 376 2.01 REMARK 500 O1A HEM A 601 O HOH A 701 2.12 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 ASP A 377 C - N - CA ANGL. DEV. = 16.2 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 PHE A 232 -61.84 -128.11 REMARK 500 ARG A 345 11.89 -144.75 REMARK 500 ARG A 345 16.52 -143.52 REMARK 500 HIS A 348 78.12 -152.51 REMARK 500 ARG A 372 -126.39 47.98 REMARK 500 ASP A 377 -33.26 -167.53 REMARK 500 TRP A 435 -71.40 -114.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 160 LYS A 161 -149.91 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 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 365 NE2 REMARK 620 2 HEM A 601 NA 91.0 REMARK 620 3 HEM A 601 NB 91.9 89.2 REMARK 620 4 HEM A 601 NC 92.2 176.1 88.4 REMARK 620 5 HEM A 601 ND 91.2 92.0 176.6 90.2 REMARK 620 6 OXY A 610 O1 176.2 91.5 85.2 85.2 91.6 REMARK 620 N 1 2 3 4 5 DBREF 7ANV A 24 511 PDB 7ANV 7ANV 24 511 SEQRES 1 A 488 ALA PRO LEU ASP LEU ASN ASN ILE GLN GLY ASP ILE LEU SEQRES 2 A 488 GLY GLY LEU PRO LYS LYS THR GLU THR TYR PHE PHE PHE SEQRES 3 A 488 LYS ILE THR ASP ALA ALA ALA PHE ARG LYS HIS LEU LYS SEQRES 4 A 488 GLN LEU ILE PRO LEU ILE THR THR THR ALA GLN VAL GLN SEQRES 5 A 488 LYS ASP ARG LYS ALA ILE ASP GLU HIS LYS LYS SER ASN SEQRES 6 A 488 GLN LYS SER GLY LYS PRO PRO GLU LEU LEU PRO LEU ALA SEQRES 7 A 488 GLY VAL ASN ILE ALA PHE SER HIS ALA GLY LEU LYS LYS SEQRES 8 A 488 LEU GLY ILE ASN ASP ASP ASN LEU GLY ASP THR ALA PHE SEQRES 9 A 488 LYS ALA GLY GLN LEU ALA ASP ALA GLN ASN LEU GLY ASP SEQRES 10 A 488 PRO GLY THR GLY ASN ALA GLY ALA LYS PHE VAL PRO ASP SEQRES 11 A 488 TRP ASP PRO ALA PHE LYS GLU LYS ASP ILE HIS GLY VAL SEQRES 12 A 488 ILE LEU VAL ALA GLY ASP SER HIS GLU THR VAL ASP LYS SEQRES 13 A 488 LYS LEU GLN GLU ILE GLU ALA ILE PHE GLY VAL GLY GLY SEQRES 14 A 488 PRO HIS ALA SER ILE HIS GLU VAL LEU THR ILE GLN GLY SEQRES 15 A 488 ASP VAL ARG PRO GLY ASP GLU LYS GLY HIS GLU HIS PHE SEQRES 16 A 488 GLY PHE GLN ASP GLY ILE SER GLN PRO ALA VAL LYS GLY SEQRES 17 A 488 PHE ASP THR ASN PRO ASN PRO GLY GLN ALA PRO VAL ARG SEQRES 18 A 488 PRO GLY VAL ILE LEU VAL GLY ARG ASP GLY ASP SER VAL SEQRES 19 A 488 ALA ASN ASN ALA ARG PRO SER TRP ALA LYS ASP GLY SER SEQRES 20 A 488 PHE LEU VAL PHE ARG LYS LEU GLN GLN LEU VAL PRO GLU SEQRES 21 A 488 PHE ASN LYS PHE LEU GLU GLU ASN PRO ILE LYS LEU PRO SEQRES 22 A 488 GLY ASN ASN LEU THR PRO GLU GLU GLY SER GLU LEU LEU SEQRES 23 A 488 GLY ALA ARG LEU VAL GLY ARG TRP LYS SER GLY ALA PRO SEQRES 24 A 488 ILE ASP ILE THR PRO LEU GLN ASP ASP PRO GLU LEU ALA SEQRES 25 A 488 LYS ASP PRO GLN ARG ASN ASN ASN PHE ARG PHE ASP HIS SEQRES 26 A 488 PRO PHE ALA ASP GLU GLN ASP SER GLN THR ARG CYS PRO SEQRES 27 A 488 PHE ALA ALA HIS ILE ARG LYS THR ASN PRO ARG ALA ASP SEQRES 28 A 488 LEU GLU ASP ALA SER PRO THR SER VAL GLU SER ARG ARG SEQRES 29 A 488 ILE ILE ARG ARG GLY ILE PRO TYR GLY PRO GLU VAL THR SEQRES 30 A 488 PRO GLU GLU LYS GLU SER LYS LYS THR LYS HIS ASP ARG SEQRES 31 A 488 GLY LEU LEU PHE VAL CYS TYR GLN SER ASN ILE GLU ASN SEQRES 32 A 488 GLY PHE GLN PHE ILE GLN LYS SER TRP ALA ASN ASN PRO SEQRES 33 A 488 ASN PHE PRO PRO SER LYS PRO ASN PRO VAL THR PRO GLY SEQRES 34 A 488 PHE ASP PRO ILE ILE GLY GLN ALA ALA ASN ASN ASP GLY SEQRES 35 A 488 ALA ARG THR MET SER GLY THR ASP PRO ASN ASN GLN ALA SEQRES 36 A 488 ASN GLU LEU SER LEU PRO THR GLU LEU PHE VAL VAL PRO SEQRES 37 A 488 ARG GLY GLY GLU TYR PHE PHE SER PRO SER ILE SER ALA SEQRES 38 A 488 LEU LYS ASP THR PHE ALA ALA HET HEM A 601 43 HET GOL A 602 6 HET SO4 A 603 5 HET SO4 A 604 5 HET SO4 A 605 5 HET SO4 A 606 5 HET SO4 A 607 5 HET SO4 A 608 5 HET SO4 A 609 5 HET OXY A 610 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM OXY OXYGEN MOLECULE HETSYN HEM HEME HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 GOL C3 H8 O3 FORMUL 4 SO4 7(O4 S 2-) FORMUL 11 OXY O2 FORMUL 12 HOH *398(H2 O) HELIX 1 AA1 ASP A 53 ILE A 65 1 13 HELIX 2 AA2 PRO A 66 ILE A 68 5 3 HELIX 3 AA3 THR A 70 GLU A 83 1 14 HELIX 4 AA4 SER A 108 GLY A 116 1 9 HELIX 5 AA5 ASP A 124 GLY A 130 1 7 HELIX 6 AA6 GLY A 130 GLY A 139 1 10 HELIX 7 AA7 ASP A 155 LYS A 161 1 7 HELIX 8 AA8 SER A 173 PHE A 188 1 16 HELIX 9 AA9 PRO A 209 LYS A 213 5 5 HELIX 10 AB1 ARG A 244 ILE A 248 5 5 HELIX 11 AB2 PRO A 263 LYS A 267 5 5 HELIX 12 AB3 LEU A 280 ASN A 291 1 12 HELIX 13 AB4 THR A 301 GLY A 315 1 15 HELIX 14 AB5 ASP A 331 LYS A 336 1 6 HELIX 15 AB6 ALA A 364 ASN A 370 1 7 HELIX 16 AB7 PRO A 371 LEU A 375 5 5 HELIX 17 AB8 SER A 379 SER A 385 1 7 HELIX 18 AB9 THR A 400 LYS A 407 1 8 HELIX 19 AC1 GLY A 427 TRP A 435 1 9 HELIX 20 AC2 SER A 501 THR A 508 1 8 SHEET 1 AA1 4 ALA A 101 PHE A 107 0 SHEET 2 AA1 4 GLY A 165 GLY A 171 -1 O ALA A 170 N GLY A 102 SHEET 3 AA1 4 THR A 43 ILE A 51 -1 N PHE A 47 O ILE A 167 SHEET 4 AA1 4 ILE A 197 ASP A 206 -1 O GLY A 205 N GLU A 44 SHEET 1 AA2 2 ALA A 228 VAL A 229 0 SHEET 2 AA2 2 PRO A 242 VAL A 243 1 O VAL A 243 N ALA A 228 SHEET 1 AA3 3 ILE A 389 ARG A 390 0 SHEET 2 AA3 3 GLY A 414 GLN A 421 -1 O TYR A 420 N ILE A 389 SHEET 3 AA3 3 ILE A 393 TYR A 395 -1 N ILE A 393 O LEU A 416 SHEET 1 AA4 4 ILE A 389 ARG A 390 0 SHEET 2 AA4 4 GLY A 414 GLN A 421 -1 O TYR A 420 N ILE A 389 SHEET 3 AA4 4 SER A 270 GLN A 279 -1 N VAL A 273 O CYS A 419 SHEET 4 AA4 4 VAL A 489 SER A 499 -1 O ARG A 492 N LYS A 276 SHEET 1 AA5 2 THR A 468 MET A 469 0 SHEET 2 AA5 2 LEU A 481 SER A 482 -1 O LEU A 481 N MET A 469 LINK NE2 HIS A 365 FE HEM A 601 1555 1555 2.03 LINK FE HEM A 601 O1 OXY A 610 1555 1555 2.24 CISPEP 1 HIS A 348 PRO A 349 0 9.66 CISPEP 2 PHE A 441 PRO A 442 0 -7.59 CRYST1 59.085 69.107 114.390 90.00 90.00 90.00 P 21 21 21 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 0.016925 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008742 0.00000