HEADER OXIDOREDUCTASE 22-JUL-23 8K5M OBSLTE 13-MAR-24 8K5M 8Y9X TITLE STRUCTURAL EVIDENCE FOR THE ORDER OF PREFERENCE OF INORGANIC TITLE 2 SUBSTRATES IN MAMMALIAN HEME PEROXIDASES: CRYSTAL STRUCTURE OF THE TITLE 3 COMPLEX OF LACTOPEROXIDASE WITH FOUR INORGANIC SUBSTRATES, SCN, I, BR TITLE 4 AND CL COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOPEROXIDASE; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.VISWANATHAN,A.K.SINGH,N.PANDEY,M.SINHA,P.KAUR,S.SHARMA,T.P.SINGH REVDAT 2 13-MAR-24 8K5M 1 OBSLTE REVDAT 1 16-AUG-23 8K5M 0 SPRSDE 16-AUG-23 8K5M 3S4F JRNL AUTH V.VISWANATHAN,A.K.SINGH,N.PANDEY,M.SINHA,P.KAUR,S.SHARMA, JRNL AUTH 2 T.P.SINGH JRNL TITL STRUCTURAL EVIDENCE FOR THE ORDER OF PREFERENCE OF INORGANIC JRNL TITL 2 SUBSTRATES IN MAMMALIAN HEME PEROXIDASES: CRYSTAL STRUCTURE JRNL TITL 3 OF THE COMPLEX OF LACTOPEROXIDASE WITH FOUR INORGANIC JRNL TITL 4 SUBSTRATES, SCN, I, BR AND CL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0415 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 39294 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.016 REMARK 3 FREE R VALUE TEST SET COUNT : 1971 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2248 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4746 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 204 REMARK 3 SOLVENT ATOMS : 405 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02300 REMARK 3 B22 (A**2) : 0.04200 REMARK 3 B33 (A**2) : -0.01300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.00800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.201 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.163 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5099 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4761 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6904 ; 1.503 ; 1.679 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10974 ; 1.525 ; 1.589 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 597 ; 6.682 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 37 ; 8.310 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 826 ;15.844 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 731 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6002 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1219 ; 0.024 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1138 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 84 ; 0.287 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2476 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 350 ; 0.169 ; 0.200 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): 2384 ; 2.758 ; 2.503 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2379 ; 2.758 ; 2.501 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2971 ; 4.318 ; 4.491 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2972 ; 4.318 ; 4.492 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2715 ; 3.140 ; 2.933 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2716 ; 3.139 ; 2.935 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3931 ; 5.112 ; 5.221 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3932 ; 5.112 ; 5.222 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8K5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39294 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 43.521 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 29.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31000 REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM IODIDE, 20%(W/V) PEG REMARK 280 3350, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 40.16600 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL 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 MET A -116 REMARK 465 TRP A -115 REMARK 465 VAL A -114 REMARK 465 CYS A -113 REMARK 465 LEU A -112 REMARK 465 GLN A -111 REMARK 465 LEU A -110 REMARK 465 PRO A -109 REMARK 465 VAL A -108 REMARK 465 PHE A -107 REMARK 465 LEU A -106 REMARK 465 ALA A -105 REMARK 465 SER A -104 REMARK 465 VAL A -103 REMARK 465 THR A -102 REMARK 465 LEU A -101 REMARK 465 PHE A -100 REMARK 465 GLU A -99 REMARK 465 VAL A -98 REMARK 465 ALA A -97 REMARK 465 ALA A -96 REMARK 465 SER A -95 REMARK 465 ASP A -94 REMARK 465 THR A -93 REMARK 465 ILE A -92 REMARK 465 ALA A -91 REMARK 465 GLN A -90 REMARK 465 ALA A -89 REMARK 465 ALA A -88 REMARK 465 SER A -87 REMARK 465 THR A -86 REMARK 465 THR A -85 REMARK 465 THR A -84 REMARK 465 ILE A -83 REMARK 465 SER A -82 REMARK 465 ASP A -81 REMARK 465 ALA A -80 REMARK 465 VAL A -79 REMARK 465 SER A -78 REMARK 465 LYS A -77 REMARK 465 VAL A -76 REMARK 465 LYS A -75 REMARK 465 ILE A -74 REMARK 465 GLN A -73 REMARK 465 VAL A -72 REMARK 465 ASN A -71 REMARK 465 LYS A -70 REMARK 465 ALA A -69 REMARK 465 PHE A -68 REMARK 465 LEU A -67 REMARK 465 ASP A -66 REMARK 465 SER A -65 REMARK 465 ARG A -64 REMARK 465 THR A -63 REMARK 465 ARG A -62 REMARK 465 LEU A -61 REMARK 465 LYS A -60 REMARK 465 THR A -59 REMARK 465 THR A -58 REMARK 465 LEU A -57 REMARK 465 SER A -56 REMARK 465 SER A -55 REMARK 465 GLU A -54 REMARK 465 ALA A -53 REMARK 465 PRO A -52 REMARK 465 THR A -51 REMARK 465 THR A -50 REMARK 465 GLN A -49 REMARK 465 GLN A -48 REMARK 465 LEU A -47 REMARK 465 SER A -46 REMARK 465 GLU A -45 REMARK 465 TYR A -44 REMARK 465 PHE A -43 REMARK 465 LYS A -42 REMARK 465 HIS A -41 REMARK 465 ALA A -40 REMARK 465 LYS A -39 REMARK 465 GLY A -38 REMARK 465 ARG A -37 REMARK 465 THR A -36 REMARK 465 ARG A -35 REMARK 465 THR A -34 REMARK 465 ALA A -33 REMARK 465 ILE A -32 REMARK 465 ARG A -31 REMARK 465 ASN A -30 REMARK 465 GLY A -29 REMARK 465 GLN A -28 REMARK 465 VAL A -27 REMARK 465 TRP A -26 REMARK 465 GLU A -25 REMARK 465 GLU A -24 REMARK 465 SER A -23 REMARK 465 LEU A -22 REMARK 465 LYS A -21 REMARK 465 ARG A -20 REMARK 465 LEU A -19 REMARK 465 ARG A -18 REMARK 465 ARG A -17 REMARK 465 ASP A -16 REMARK 465 THR A -15 REMARK 465 THR A -14 REMARK 465 LEU A -13 REMARK 465 THR A -12 REMARK 465 ASN A -11 REMARK 465 VAL A -10 REMARK 465 THR A -9 REMARK 465 ASP A -8 REMARK 465 PRO A -7 REMARK 465 SER A -6 REMARK 465 LEU A -5 REMARK 465 ASP A -4 REMARK 465 LEU A -3 REMARK 465 THR A -2 REMARK 465 ALA A -1 REMARK 465 LEU A 0 REMARK 465 ARG A 593 REMARK 465 GLU A 594 REMARK 465 ASN A 595 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 C4 NAG A 627 O1 NAG A 628 1.71 REMARK 500 O4 NAG A 630 C1 NAG A 631 1.94 REMARK 500 OE2 GLU A 130 O HOH A 701 2.13 REMARK 500 OG SER A 235 O HOH A 702 2.18 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 HIS A 426 CB - CA - C ANGL. DEV. = 12.3 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 GLU A 3 -123.11 49.71 REMARK 500 SER A 19 66.87 38.59 REMARK 500 ALA A 56 -16.08 -146.57 REMARK 500 LEU A 119 -138.95 60.51 REMARK 500 ASP A 137 -124.94 55.11 REMARK 500 CYS A 167 -92.68 93.04 REMARK 500 ASP A 188 17.39 -140.60 REMARK 500 PRO A 209 44.88 -83.44 REMARK 500 LYS A 232 127.29 -173.12 REMARK 500 ASN A 241 97.62 -160.14 REMARK 500 GLU A 371 44.47 -106.36 REMARK 500 ASP A 389 45.67 -142.47 REMARK 500 ASN A 473 114.87 -162.79 REMARK 500 LYS A 485 -28.41 79.32 REMARK 500 PRO A 533 134.21 -35.94 REMARK 500 PRO A 589 -9.82 -56.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 177 0.14 SIDE CHAIN 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 A1105 DISTANCE = 5.94 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG A 627 REMARK 610 NAG A 631 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 CA A 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 110 O REMARK 620 2 ASP A 110 OD2 74.0 REMARK 620 3 THR A 184 O 74.0 136.9 REMARK 620 4 THR A 184 OG1 131.9 150.7 71.4 REMARK 620 5 PHE A 186 O 114.7 80.1 87.8 96.3 REMARK 620 6 ASP A 188 OD1 144.8 77.0 140.9 73.7 78.9 REMARK 620 7 SER A 190 OG 82.3 88.4 114.9 83.0 155.4 77.3 REMARK 620 N 1 2 3 4 5 6 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 351 NE2 REMARK 620 2 HEM A 601 NA 97.0 REMARK 620 3 HEM A 601 NB 98.5 87.5 REMARK 620 4 HEM A 601 NC 87.3 175.1 89.6 REMARK 620 5 HEM A 601 ND 86.1 90.5 175.2 92.1 REMARK 620 6 HOH A 816 O 173.6 77.4 84.5 98.4 90.7 REMARK 620 N 1 2 3 4 5 DBREF 8K5M A -116 595 UNP P80025 PERL_BOVIN 1 712 SEQRES 1 A 712 MET TRP VAL CYS LEU GLN LEU PRO VAL PHE LEU ALA SER SEQRES 2 A 712 VAL THR LEU PHE GLU VAL ALA ALA SER ASP THR ILE ALA SEQRES 3 A 712 GLN ALA ALA SER THR THR THR ILE SER ASP ALA VAL SER SEQRES 4 A 712 LYS VAL LYS ILE GLN VAL ASN LYS ALA PHE LEU ASP SER SEQRES 5 A 712 ARG THR ARG LEU LYS THR THR LEU SER SER GLU ALA PRO SEQRES 6 A 712 THR THR GLN GLN LEU SER GLU TYR PHE LYS HIS ALA LYS SEQRES 7 A 712 GLY ARG THR ARG THR ALA ILE ARG ASN GLY GLN VAL TRP SEQRES 8 A 712 GLU GLU SER LEU LYS ARG LEU ARG ARG ASP THR THR LEU SEQRES 9 A 712 THR ASN VAL THR ASP PRO SER LEU ASP LEU THR ALA LEU SEQRES 10 A 712 SER TRP GLU VAL GLY CYS GLY ALA PRO VAL PRO LEU VAL SEQRES 11 A 712 LYS CYS ASP GLU ASN SER PRO TYR ARG THR ILE THR GLY SEQRES 12 A 712 ASP CYS ASN ASN ARG ARG SER PRO ALA LEU GLY ALA ALA SEQRES 13 A 712 ASN ARG ALA LEU ALA ARG TRP LEU PRO ALA GLU TYR GLU SEQRES 14 A 712 ASP GLY LEU ALA LEU PRO PHE GLY TRP THR GLN ARG LYS SEQRES 15 A 712 THR ARG ASN GLY PHE ARG VAL PRO LEU ALA ARG GLU VAL SEQRES 16 A 712 SER ASN LYS ILE VAL GLY TYR LEU ASP GLU GLU GLY VAL SEQRES 17 A 712 LEU ASP GLN ASN ARG SER LEU LEU PHE MET GLN TRP GLY SEQRES 18 A 712 GLN ILE VAL ASP HIS ASP LEU ASP PHE ALA PRO GLU THR SEQRES 19 A 712 GLU LEU GLY SER ASN GLU HIS SER LYS THR GLN CYS GLU SEQRES 20 A 712 GLU TYR CYS ILE GLN GLY ASP ASN CYS PHE PRO ILE MET SEQRES 21 A 712 PHE PRO LYS ASN ASP PRO LYS LEU LYS THR GLN GLY LYS SEQRES 22 A 712 CYS MET PRO PHE PHE ARG ALA GLY PHE VAL CYS PRO THR SEQRES 23 A 712 PRO PRO TYR GLN SER LEU ALA ARG GLU GLN ILE ASN ALA SEQRES 24 A 712 VAL THR SER PHE LEU ASP ALA SER LEU VAL TYR GLY SER SEQRES 25 A 712 GLU PRO SEP LEU ALA SER ARG LEU ARG ASN LEU SER SER SEQRES 26 A 712 PRO LEU GLY LEU MET ALA VAL ASN GLN GLU ALA TRP ASP SEQRES 27 A 712 HIS GLY LEU ALA TYR LEU PRO PHE ASN ASN LYS LYS PRO SEQRES 28 A 712 SER PRO CYS GLU PHE ILE ASN THR THR ALA ARG VAL PRO SEQRES 29 A 712 CYS PHE LEU ALA GLY ASP PHE ARG ALA SER GLU GLN ILE SEQRES 30 A 712 LEU LEU ALA THR ALA HIS THR LEU LEU LEU ARG GLU HIS SEQRES 31 A 712 ASN ARG LEU ALA ARG GLU LEU LYS LYS LEU ASN PRO HIS SEQRES 32 A 712 TRP ASN GLY GLU LYS LEU TYR GLN GLU ALA ARG LYS ILE SEQRES 33 A 712 LEU GLY ALA PHE ILE GLN ILE ILE THR PHE ARG ASP TYR SEQRES 34 A 712 LEU PRO ILE VAL LEU GLY SER GLU MET GLN LYS TRP ILE SEQRES 35 A 712 PRO PRO TYR GLN GLY TYR ASN ASN SER VAL ASP PRO ARG SEQRES 36 A 712 ILE SER ASN VAL PHE THR PHE ALA PHE ARG PHE GLY HIS SEQRES 37 A 712 MET GLU VAL PRO SER THR VAL SER ARG LEU ASP GLU ASN SEQRES 38 A 712 TYR GLN PRO TRP GLY PRO GLU ALA GLU LEU PRO LEU HIS SEQRES 39 A 712 THR LEU PHE PHE ASN THR TRP ARG ILE ILE LYS ASP GLY SEQRES 40 A 712 GLY ILE ASP PRO LEU VAL ARG GLY LEU LEU ALA LYS LYS SEQRES 41 A 712 SER LYS LEU MET ASN GLN ASP LYS MET VAL THR SER GLU SEQRES 42 A 712 LEU ARG ASN LYS LEU PHE GLN PRO THR HIS LYS ILE HIS SEQRES 43 A 712 GLY PHE ASP LEU ALA ALA ILE ASN LEU GLN ARG CYS ARG SEQRES 44 A 712 ASP HIS GLY MET PRO GLY TYR ASN SER TRP ARG GLY PHE SEQRES 45 A 712 CYS GLY LEU SER GLN PRO LYS THR LEU LYS GLY LEU GLN SEQRES 46 A 712 THR VAL LEU LYS ASN LYS ILE LEU ALA LYS LYS LEU MET SEQRES 47 A 712 ASP LEU TYR LYS THR PRO ASP ASN ILE ASP ILE TRP ILE SEQRES 48 A 712 GLY GLY ASN ALA GLU PRO MET VAL GLU ARG GLY ARG VAL SEQRES 49 A 712 GLY PRO LEU LEU ALA CYS LEU LEU GLY ARG GLN PHE GLN SEQRES 50 A 712 GLN ILE ARG ASP GLY ASP ARG PHE TRP TRP GLU ASN PRO SEQRES 51 A 712 GLY VAL PHE THR GLU LYS GLN ARG ASP SER LEU GLN LYS SEQRES 52 A 712 VAL SER PHE SER ARG LEU ILE CYS ASP ASN THR HIS ILE SEQRES 53 A 712 THR LYS VAL PRO LEU HIS ALA PHE GLN ALA ASN ASN TYR SEQRES 54 A 712 PRO HIS ASP PHE VAL ASP CYS SER THR VAL ASP LYS LEU SEQRES 55 A 712 ASP LEU SER PRO TRP ALA SER ARG GLU ASN MODRES 8K5M SEP A 198 SER MODIFIED RESIDUE HET SEP A 198 10 HET HEM A 601 43 HET CA A 602 1 HET IOD A 603 2 HET IOD A 604 1 HET IOD A 605 2 HET IOD A 606 1 HET IOD A 607 2 HET IOD A 608 1 HET IOD A 609 2 HET IOD A 610 1 HET BR A 611 1 HET CL A 612 1 HET IOD A 613 2 HET SCN A 614 3 HET PEG A 615 7 HET PEG A 616 7 HET PEG A 617 7 HET PEG A 618 7 HET PEG A 619 7 HET PEG A 620 7 HET PEG A 621 7 HET SCN A 622 3 HET SCN A 623 3 HET SCN A 624 3 HET SCN A 625 3 HET NAG A 626 14 HET NAG A 627 13 HET NAG A 628 15 HET NAG A 629 14 HET NAG A 630 14 HET NAG A 631 14 HET IOD A 632 2 HETNAM SEP PHOSPHOSERINE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CA CALCIUM ION HETNAM IOD IODIDE ION HETNAM BR BROMIDE ION HETNAM CL CHLORIDE ION HETNAM SCN THIOCYANATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN SEP PHOSPHONOSERINE HETSYN HEM HEME HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CA CA 2+ FORMUL 4 IOD 10(I 1-) FORMUL 12 BR BR 1- FORMUL 13 CL CL 1- FORMUL 15 SCN 5(C N S 1-) FORMUL 16 PEG 7(C4 H10 O3) FORMUL 27 NAG 6(C8 H15 N O6) FORMUL 34 HOH *405(H2 O) HELIX 1 AA1 LEU A 74 VAL A 83 1 10 HELIX 2 AA2 LEU A 98 ASP A 112 1 15 HELIX 3 AA3 ASN A 122 CYS A 133 1 12 HELIX 4 AA4 LYS A 150 GLY A 155 1 6 HELIX 5 AA5 ALA A 189 GLY A 194 1 6 HELIX 6 AA6 GLU A 196 ARG A 204 1 9 HELIX 7 AA7 SER A 235 ILE A 240 1 6 HELIX 8 AA8 GLN A 259 ASN A 284 1 26 HELIX 9 AA9 ASN A 288 ASP A 311 1 24 HELIX 10 AB1 TYR A 312 GLY A 318 1 7 HELIX 11 AB2 GLU A 320 ILE A 325 1 6 HELIX 12 AB3 VAL A 342 PHE A 347 1 6 HELIX 13 AB4 ARG A 348 VAL A 354 5 7 HELIX 14 AB5 HIS A 377 PHE A 380 5 4 HELIX 15 AB6 THR A 383 LYS A 388 1 6 HELIX 16 AB7 ILE A 392 LYS A 402 1 11 HELIX 17 AB8 THR A 414 ASN A 419 1 6 HELIX 18 AB9 ASP A 432 HIS A 444 1 13 HELIX 19 AC1 GLY A 448 CYS A 456 1 9 HELIX 20 AC2 THR A 463 LYS A 472 1 10 HELIX 21 AC3 ASN A 473 LYS A 485 1 13 HELIX 22 AC4 THR A 486 ILE A 490 5 5 HELIX 23 AC5 ASP A 491 ALA A 498 1 8 HELIX 24 AC6 GLY A 508 GLY A 525 1 18 HELIX 25 AC7 THR A 537 GLN A 545 1 9 HELIX 26 AC8 SER A 548 THR A 557 1 10 HELIX 27 AC9 SER A 580 VAL A 582 5 3 HELIX 28 AD1 LEU A 587 ALA A 591 5 5 SHEET 1 AA1 2 ARG A 41 ALA A 42 0 SHEET 2 AA1 2 ILE A 180 ASN A 181 -1 O ASN A 181 N ARG A 41 SHEET 1 AA2 2 LEU A 92 SER A 97 0 SHEET 2 AA2 2 LYS A 403 LYS A 405 -1 O SER A 404 N ASP A 93 SHEET 1 AA3 2 ILE A 142 MET A 143 0 SHEET 2 AA3 2 CYS A 157 MET A 158 -1 O MET A 158 N ILE A 142 SHEET 1 AA4 2 THR A 357 SER A 359 0 SHEET 2 AA4 2 GLU A 373 PRO A 375 -1 O LEU A 374 N VAL A 358 SHEET 1 AA5 2 LEU A 421 PHE A 422 0 SHEET 2 AA5 2 HIS A 429 PHE A 431 -1 O PHE A 431 N LEU A 421 SHEET 1 AA6 2 LYS A 561 PRO A 563 0 SHEET 2 AA6 2 PHE A 576 ASP A 578 -1 O VAL A 577 N VAL A 562 SSBOND 1 CYS A 6 CYS A 167 1555 1555 2.24 SSBOND 2 CYS A 15 CYS A 28 1555 1555 2.07 SSBOND 3 CYS A 129 CYS A 139 1555 1555 2.05 SSBOND 4 CYS A 133 CYS A 157 1555 1555 2.10 SSBOND 5 CYS A 237 CYS A 248 1555 1555 2.09 SSBOND 6 CYS A 456 CYS A 513 1555 1555 2.10 SSBOND 7 CYS A 554 CYS A 579 1555 1555 2.05 LINK ND2 ASN A 95 C1 NAG A 626 1555 1555 1.46 LINK OD2 ASP A 108 CMD HEM A 601 1555 1555 1.40 LINK C PRO A 197 N SEP A 198 1555 1555 1.33 LINK C SEP A 198 N LEU A 199 1555 1555 1.33 LINK ND2 ASN A 205 C1 NAG A 630 1555 1555 1.45 LINK ND2 ASN A 241 C1 NAG A 627 1555 1555 1.46 LINK OE2 GLU A 258 CMB HEM A 601 1555 1555 1.44 LINK ND2 ASN A 332 C1 NAG A 629 1555 1555 1.49 LINK O ASP A 110 CA CA A 602 1555 1555 2.40 LINK OD2 ASP A 110 CA CA A 602 1555 1555 2.41 LINK O THR A 184 CA CA A 602 1555 1555 2.43 LINK OG1 THR A 184 CA CA A 602 1555 1555 2.42 LINK O PHE A 186 CA CA A 602 1555 1555 2.38 LINK OD1 ASP A 188 CA CA A 602 1555 1555 2.43 LINK OG SER A 190 CA CA A 602 1555 1555 2.42 LINK NE2 HIS A 351 FE HEM A 601 1555 1555 2.16 LINK FE HEM A 601 O HOH A 816 1555 1555 2.24 CISPEP 1 LYS A 233 PRO A 234 0 -7.69 CISPEP 2 TYR A 572 PRO A 573 0 5.56 CRYST1 53.350 80.332 73.391 90.00 103.94 90.00 P 1 21 1 2 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 0.018744 0.000000 0.004653 0.00000 SCALE2 0.000000 0.012448 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014039 0.00000