HEADER OXIDOREDUCTASE 17-DEC-13 3WNU TITLE THE CRYSTAL STRUCTURE OF CATALASE-PEROXIDASE, KATG, FROM SYNECHOCOCCUS TITLE 2 PCC7942 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATALASE-PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALASE-PEROXIDASE; COMPND 5 SYNONYM: CP, PEROXIDASE/CATALASE; COMPND 6 EC: 1.11.1.21; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS; SOURCE 3 ORGANISM_TAXID: 1140; SOURCE 4 STRAIN: PCC 7942; SOURCE 5 GENE: KATG, SYNPCC7942_1656; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS PEROXIDASE FAMILY, PEROXIDASE/CATALASE SUBFAMILY, OXIDOREDUCTASE, KEYWDS 2 HEME B, FE, CROSS-LINK, COVALENT TRP-TYR-MET ADDUCT EXPDTA X-RAY DIFFRACTION AUTHOR T.TADA,K.WADA,S.KAMACHI REVDAT 3 20-MAR-24 3WNU 1 REMARK LINK REVDAT 2 18-DEC-19 3WNU 1 JRNL REVDAT 1 12-MAR-14 3WNU 0 JRNL AUTH S.KAMACHI,K.WADA,M.TAMOI,S.SHIGEOKA,T.TADA JRNL TITL THE 2.2 ANGSTROM RESOLUTION STRUCTURE OF THE JRNL TITL 2 CATALASE-PEROXIDASE KATG FROM SYNECHOCOCCUS ELONGATUS JRNL TITL 3 PCC7942. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 70 288 2014 JRNL REFN ESSN 2053-230X JRNL PMID 24598912 JRNL DOI 10.1107/S2053230X14002052 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 59197 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3158 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4273 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 248 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5582 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 522 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.11000 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): 0.158 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.902 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5779 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5318 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7885 ; 2.038 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12209 ; 1.007 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 709 ; 6.498 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 283 ;34.821 ;24.205 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 901 ;16.976 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;18.991 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 822 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6696 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1375 ; 0.007 ; 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): 2839 ; 3.158 ; 3.480 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2838 ; 3.137 ; 3.479 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3547 ; 4.305 ; 5.206 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3548 ; 4.307 ; 5.207 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2939 ; 3.943 ; 3.738 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2937 ; 3.944 ; 3.739 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4338 ; 5.592 ; 5.487 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7586 ; 6.941 ;28.907 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7363 ; 6.913 ;28.647 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 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3WNU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000096569. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63054 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 35.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.15500 REMARK 200 R SYM FOR SHELL (I) : 0.28600 REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 67.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE, PH 6.3, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.44400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 54.37200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.37200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.72200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.37200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.37200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 152.16600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.37200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.37200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.72200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.37200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.37200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 152.16600 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 101.44400 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: 12350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -202.88800 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 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 THR A 4 REMARK 465 GLN A 5 REMARK 465 GLY A 6 REMARK 465 LYS A 7 REMARK 465 CYS A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 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 CH2 TRP A 94 CE2 TYR A 222 1.83 REMARK 500 CE1 TYR A 222 SD MET A 248 1.92 REMARK 500 N ASP A 48 O HOH A 1421 2.16 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 1332 O HOH A 1334 7554 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 287 CD GLU A 287 OE1 0.085 REMARK 500 ARG A 327 NE ARG A 327 CZ 0.126 REMARK 500 ARG A 327 CZ ARG A 327 NH2 0.080 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 THR A 99 N - CA - CB ANGL. DEV. = -13.3 DEGREES REMARK 500 ASP A 124 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 LEU A 165 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 ARG A 242 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 242 NE - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 LEU A 310 CB - CG - CD2 ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG A 327 CG - CD - NE ANGL. DEV. = 21.7 DEGREES REMARK 500 ARG A 327 NH1 - CZ - NH2 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 327 NE - CZ - NH2 ANGL. DEV. = 9.0 DEGREES REMARK 500 GLU A 353 CB - CA - C ANGL. DEV. = -12.6 DEGREES REMARK 500 VAL A 370 CB - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 ARG A 385 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 412 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 MET A 414 CG - SD - CE ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 502 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 538 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 VAL A 567 CG1 - CB - CG2 ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG A 576 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 576 NE - CZ - NH2 ANGL. DEV. = -8.5 DEGREES REMARK 500 LEU A 608 CB - CG - CD1 ANGL. DEV. = 11.0 DEGREES REMARK 500 THR A 628 CB - CA - C ANGL. DEV. = -19.0 DEGREES REMARK 500 THR A 643 N - CA - CB ANGL. DEV. = -13.1 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 ASP A 73 72.68 -115.47 REMARK 500 TRP A 78 81.30 -156.78 REMARK 500 TYR A 222 -72.95 -128.80 REMARK 500 ASP A 233 97.79 -172.93 REMARK 500 THR A 307 -85.76 -129.36 REMARK 500 ASP A 322 -170.26 -171.28 REMARK 500 ARG A 367 -142.53 -123.87 REMARK 500 ALA A 652 54.06 -146.04 REMARK 500 SER A 680 -54.07 -128.50 REMARK 500 ARG A 716 53.70 -93.43 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 210 ASN A 211 -140.09 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 NA A 802 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 105 O REMARK 620 2 GLY A 107 O 101.3 REMARK 620 3 SER A 476 O 89.4 156.5 REMARK 620 4 HOH A1078 O 104.9 100.8 96.4 REMARK 620 5 HOH A1325 O 166.6 79.3 85.5 88.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEB A 801 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 263 NE2 REMARK 620 2 HEB A 801 NA 96.4 REMARK 620 3 HEB A 801 NB 90.8 94.4 REMARK 620 4 HEB A 801 NC 86.1 177.5 85.3 REMARK 620 5 HEB A 801 ND 91.5 85.6 177.7 94.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 803 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 264 O REMARK 620 2 THR A 315 OG1 74.8 REMARK 620 3 HIS A 317 O 120.7 80.7 REMARK 620 4 GLN A 320 O 96.4 161.2 90.0 REMARK 620 5 ASP A 322 OD2 152.0 112.1 87.2 83.5 REMARK 620 6 ASP A 322 OD1 103.9 106.9 134.9 91.3 48.2 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 HEB A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 803 DBREF 3WNU A 1 720 UNP Q31MN3 KATG_SYNE7 1 720 SEQRES 1 A 720 MET THR ALA THR GLN GLY LYS CYS PRO VAL MET HIS GLY SEQRES 2 A 720 GLY ALA THR THR VAL ASN ILE SER THR ALA GLU TRP TRP SEQRES 3 A 720 PRO LYS ALA LEU ASN LEU ASP ILE LEU SER GLN HIS ASP SEQRES 4 A 720 ARG LYS THR ASN PRO MET GLY PRO ASP PHE ASN TYR GLN SEQRES 5 A 720 GLU GLU VAL LYS LYS LEU ASP VAL ALA ALA LEU LYS GLN SEQRES 6 A 720 ASP LEU GLN ALA LEU MET THR ASP SER GLN ASP TRP TRP SEQRES 7 A 720 PRO ALA ASP TRP GLY HIS TYR GLY GLY LEU MET ILE ARG SEQRES 8 A 720 LEU THR TRP HIS ALA ALA GLY THR TYR ARG ILE ALA ASP SEQRES 9 A 720 GLY ARG GLY GLY ALA GLY THR GLY ASN GLN ARG PHE ALA SEQRES 10 A 720 PRO LEU ASN SER TRP PRO ASP ASN THR ASN LEU ASP LYS SEQRES 11 A 720 ALA ARG ARG LEU LEU TRP PRO ILE LYS GLN LYS TYR GLY SEQRES 12 A 720 ASN LYS LEU SER TRP ALA ASP LEU ILE ALA TYR ALA GLY SEQRES 13 A 720 THR ILE ALA TYR GLU SER MET GLY LEU LYS THR PHE GLY SEQRES 14 A 720 PHE ALA PHE GLY ARG GLU ASP ILE TRP HIS PRO GLU LYS SEQRES 15 A 720 ASP ILE TYR TRP GLY PRO GLU LYS GLU TRP VAL PRO PRO SEQRES 16 A 720 SER THR ASN PRO ASN SER ARG TYR THR GLY ASP ARG GLU SEQRES 17 A 720 LEU GLU ASN PRO LEU ALA ALA VAL THR MET GLY LEU ILE SEQRES 18 A 720 TYR VAL ASN PRO GLU GLY VAL ASP GLY ASN PRO ASP PRO SEQRES 19 A 720 LEU LYS THR ALA HIS ASP VAL ARG VAL THR PHE ALA ARG SEQRES 20 A 720 MET ALA MET ASN ASP GLU GLU THR VAL ALA LEU THR ALA SEQRES 21 A 720 GLY GLY HIS THR VAL GLY LYS CYS HIS GLY ASN GLY ASN SEQRES 22 A 720 ALA ALA LEU LEU GLY PRO GLU PRO GLU GLY ALA ASP VAL SEQRES 23 A 720 GLU ASP GLN GLY LEU GLY TRP ILE ASN LYS THR GLN SER SEQRES 24 A 720 GLY ILE GLY ARG ASN ALA VAL THR SER GLY LEU GLU GLY SEQRES 25 A 720 ALA TRP THR PRO HIS PRO THR GLN TRP ASP ASN GLY TYR SEQRES 26 A 720 PHE ARG MET LEU LEU ASN TYR ASP TRP GLU LEU LYS LYS SEQRES 27 A 720 SER PRO ALA GLY ALA TRP GLN TRP GLU PRO ILE ASN PRO SEQRES 28 A 720 ARG GLU GLU ASP LEU PRO VAL ASP VAL GLU ASP PRO SER SEQRES 29 A 720 ILE ARG ARG ASN LEU VAL MET THR ASP ALA ASP MET ALA SEQRES 30 A 720 MET LYS MET ASP PRO GLU TYR ARG LYS ILE SER GLU ARG SEQRES 31 A 720 PHE TYR GLN ASP PRO ALA TYR PHE ALA ASP VAL PHE ALA SEQRES 32 A 720 ARG ALA TRP PHE LYS LEU THR HIS ARG ASP MET GLY PRO SEQRES 33 A 720 LYS ALA ARG TYR ILE GLY PRO ASP VAL PRO GLN GLU ASP SEQRES 34 A 720 LEU ILE TRP GLN ASP PRO ILE PRO ALA GLY ASN ARG ASN SEQRES 35 A 720 TYR ASP VAL GLN ALA VAL LYS ASP ARG ILE ALA ALA SER SEQRES 36 A 720 GLY LEU SER ILE SER GLU LEU VAL SER THR ALA TRP ASP SEQRES 37 A 720 SER ALA ARG THR TYR ARG ASN SER ASP LYS ARG GLY GLY SEQRES 38 A 720 ALA ASN GLY ALA ARG ILE ARG LEU ALA PRO GLN LYS ASP SEQRES 39 A 720 TRP GLU GLY ASN GLU PRO ASP ARG LEU ALA LYS VAL LEU SEQRES 40 A 720 ALA VAL LEU GLU GLY ILE ALA ALA ALA THR GLY ALA SER SEQRES 41 A 720 VAL ALA ASP VAL ILE VAL LEU ALA GLY ASN VAL GLY VAL SEQRES 42 A 720 GLU GLN ALA ALA ARG ALA ALA GLY VAL GLU ILE VAL LEU SEQRES 43 A 720 PRO PHE ALA PRO GLY ARG GLY ASP ALA THR ALA GLU GLN SEQRES 44 A 720 THR ASP THR GLU SER PHE ALA VAL LEU GLU PRO ILE HIS SEQRES 45 A 720 ASP GLY TYR ARG ASN TRP LEU LYS GLN ASP TYR ALA ALA SEQRES 46 A 720 THR PRO GLU GLU LEU LEU LEU ASP ARG THR GLN LEU LEU SEQRES 47 A 720 GLY LEU THR ALA PRO GLU MET THR VAL LEU ILE GLY GLY SEQRES 48 A 720 LEU ARG VAL LEU GLY THR ASN HIS GLY GLY THR LYS HIS SEQRES 49 A 720 GLY VAL PHE THR ASP ARG GLU GLY VAL LEU THR ASN ASP SEQRES 50 A 720 PHE PHE VAL ASN LEU THR ASP MET ASN TYR LEU TRP LYS SEQRES 51 A 720 PRO ALA GLY LYS ASN LEU TYR GLU ILE CYS ASP ARG LYS SEQRES 52 A 720 THR ASN GLN VAL LYS TRP THR ALA THR ARG VAL ASP LEU SEQRES 53 A 720 VAL PHE GLY SER ASN SER ILE LEU ARG ALA TYR SER GLU SEQRES 54 A 720 LEU TYR ALA GLN ASP ASP ASN LYS GLU LYS PHE VAL ARG SEQRES 55 A 720 ASP PHE VAL ALA ALA TRP THR LYS VAL MET ASN ALA ASP SEQRES 56 A 720 ARG PHE ASP LEU ASP HET HEB A 801 43 HET NA A 802 1 HET NA A 803 1 HETNAM HEB HEME B/C HETNAM NA SODIUM ION HETSYN HEB HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX HETSYN 2 HEB CONTAINING FE) FORMUL 2 HEB C34 H34 FE N4 O4 FORMUL 3 NA 2(NA 1+) FORMUL 5 HOH *522(H2 O) HELIX 1 1 ASN A 31 SER A 36 5 6 HELIX 2 2 ASN A 50 LYS A 56 1 7 HELIX 3 3 ASP A 59 MET A 71 1 13 HELIX 4 4 ALA A 80 HIS A 84 5 5 HELIX 5 5 TYR A 85 GLY A 98 1 14 HELIX 6 6 GLY A 112 PHE A 116 5 5 HELIX 7 7 PRO A 118 THR A 126 5 9 HELIX 8 8 ASN A 127 LEU A 135 1 9 HELIX 9 9 LEU A 135 GLY A 143 1 9 HELIX 10 10 ASN A 144 LEU A 146 5 3 HELIX 11 11 SER A 147 MET A 163 1 17 HELIX 12 12 GLY A 227 ASN A 231 5 5 HELIX 13 13 ASP A 233 MET A 248 1 16 HELIX 14 14 ASN A 251 THR A 264 1 14 HELIX 15 15 ASN A 273 LEU A 277 5 5 HELIX 16 16 GLU A 280 ALA A 284 5 5 HELIX 17 17 ASP A 285 GLN A 289 5 5 HELIX 18 18 ILE A 301 ALA A 305 5 5 HELIX 19 19 ASN A 323 TYR A 332 1 10 HELIX 20 20 ARG A 352 LEU A 356 5 5 HELIX 21 21 THR A 372 ASP A 381 1 10 HELIX 22 22 ASP A 381 ASP A 394 1 14 HELIX 23 23 ASP A 394 ARG A 412 1 19 HELIX 24 24 PRO A 416 TYR A 420 5 5 HELIX 25 25 LEU A 430 ASP A 434 5 5 HELIX 26 26 ASP A 444 SER A 455 1 12 HELIX 27 27 SER A 458 ARG A 471 1 14 HELIX 28 28 ALA A 485 LEU A 489 5 5 HELIX 29 29 PRO A 491 ASN A 498 5 8 HELIX 30 30 GLU A 499 GLY A 518 1 20 HELIX 31 31 SER A 520 ALA A 540 1 21 HELIX 32 32 THR A 562 GLU A 569 5 8 HELIX 33 33 GLY A 574 ASN A 577 5 4 HELIX 34 34 THR A 586 GLY A 599 1 14 HELIX 35 35 THR A 601 GLY A 616 1 16 HELIX 36 36 ASN A 618 THR A 622 5 5 HELIX 37 37 ASN A 636 THR A 643 1 8 HELIX 38 38 THR A 672 PHE A 678 1 7 HELIX 39 39 ASN A 681 GLN A 693 1 13 HELIX 40 40 ASN A 696 ASN A 713 1 18 SHEET 1 A 2 TYR A 203 THR A 204 0 SHEET 2 A 2 GLU A 208 LEU A 209 -1 O GLU A 208 N THR A 204 SHEET 1 B 2 LYS A 267 CYS A 268 0 SHEET 2 B 2 GLY A 312 ALA A 313 -1 O GLY A 312 N CYS A 268 SHEET 1 C 2 TRP A 334 LYS A 338 0 SHEET 2 C 2 TRP A 344 PRO A 348 -1 O GLU A 347 N GLU A 335 SHEET 1 D 2 HIS A 572 ASP A 573 0 SHEET 2 D 2 TRP A 578 LEU A 579 -1 O TRP A 578 N ASP A 573 SHEET 1 E 3 TYR A 647 PRO A 651 0 SHEET 2 E 3 TYR A 657 ASP A 661 -1 O CYS A 660 N LEU A 648 SHEET 3 E 3 VAL A 667 ALA A 671 -1 O LYS A 668 N ILE A 659 LINK O GLY A 105 NA NA A 802 1555 1555 2.29 LINK O GLY A 107 NA NA A 802 1555 1555 2.30 LINK NE2 HIS A 263 FE HEB A 801 1555 1555 2.19 LINK O THR A 264 NA NA A 803 1555 1555 2.40 LINK OG1 THR A 315 NA NA A 803 1555 1555 2.85 LINK O HIS A 317 NA NA A 803 1555 1555 2.33 LINK O GLN A 320 NA NA A 803 1555 1555 2.40 LINK OD2 ASP A 322 NA NA A 803 1555 1555 2.47 LINK OD1 ASP A 322 NA NA A 803 1555 1555 2.81 LINK O SER A 476 NA NA A 802 1555 1555 2.41 LINK NA NA A 802 O HOH A1078 1555 1555 2.45 LINK NA NA A 802 O HOH A1325 1555 1555 2.34 CISPEP 1 ALA A 117 PRO A 118 0 -8.64 CISPEP 2 ALA A 490 PRO A 491 0 -7.32 SITE 1 AC1 21 GLY A 87 LEU A 88 ILE A 90 ARG A 91 SITE 2 AC1 21 TRP A 94 PHE A 245 LEU A 258 THR A 259 SITE 3 AC1 21 GLY A 262 HIS A 263 GLY A 266 LYS A 267 SITE 4 AC1 21 CYS A 268 HIS A 269 THR A 307 SER A 308 SITE 5 AC1 21 TRP A 314 TRP A 406 HOH A 915 HOH A 943 SITE 6 AC1 21 HOH A 978 SITE 1 AC2 6 GLY A 105 ARG A 106 GLY A 107 SER A 476 SITE 2 AC2 6 HOH A1078 HOH A1325 SITE 1 AC3 5 THR A 264 THR A 315 HIS A 317 GLN A 320 SITE 2 AC3 5 ASP A 322 CRYST1 108.744 108.744 202.888 90.00 90.00 90.00 P 41 21 2 8 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 0.009196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004929 0.00000