HEADER OXYGEN TRANSPORT 30-JUL-10 3O7N TITLE THE V59W MUTATION BLOCKS THE DISTAL POCKET OF THE HEMOGLOBIN - TITLE 2 DEHALOPEROXIDASE FROM AMPHITRITE ORNATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEHALOPEROXIDASE A; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AMPHITRITE ORNATA; SOURCE 3 ORGANISM_TAXID: 129555; SOURCE 4 GENE: DHPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS PEROXIDASE, GLOBIN, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR V.S.DE SERRANO,M.F.DAVIS,S.FRANZEN REVDAT 2 06-SEP-23 3O7N 1 REMARK SEQADV LINK REVDAT 1 13-JUL-11 3O7N 0 JRNL AUTH M.F.DAVIS,V.S.DE SERRANO,H.GRACZ,F.A.P.VENDREIX, JRNL AUTH 2 A.SOMASUNDRAM,M.NEGRERIE,S.FRANZEN JRNL TITL THE V59W MUTATION BLOCKS THE DISTAL POCKET OF THE HEMOGLOBIN JRNL TITL 2 - DEHALOPEROXIDASE FROM AMPHITIRITE ORNATA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 26238 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1446 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) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1993 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 117 REMARK 3 SOLVENT ATOMS : 318 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : 0.07000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.091 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.023 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3138 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4371 ; 1.984 ; 2.044 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 436 ; 5.740 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;37.846 ;24.176 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 624 ;18.345 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;19.498 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 427 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2539 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1722 ; 1.015 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2858 ; 1.532 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1416 ; 2.661 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1424 ; 3.723 ; 4.500 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 : 2 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 1 A 193 REMARK 3 ORIGIN FOR THE GROUP (A): 7.4334 -4.7446 -15.1987 REMARK 3 T TENSOR REMARK 3 T11: 0.0137 T22: 0.0250 REMARK 3 T33: 0.0199 T12: 0.0011 REMARK 3 T13: 0.0040 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.1560 L22: 0.4391 REMARK 3 L33: 0.6754 L12: 0.0378 REMARK 3 L13: 0.2635 L23: -0.1624 REMARK 3 S TENSOR REMARK 3 S11: 0.0209 S12: -0.0129 S13: 0.0100 REMARK 3 S21: 0.0188 S22: -0.0336 S23: 0.0310 REMARK 3 S31: -0.0052 S32: -0.0293 S33: 0.0127 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 : B 1 B 195 REMARK 3 ORIGIN FOR THE GROUP (A): 5.7653 -31.3445 13.3180 REMARK 3 T TENSOR REMARK 3 T11: 0.0055 T22: 0.0078 REMARK 3 T33: 0.0104 T12: -0.0013 REMARK 3 T13: 0.0030 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.2839 L22: 0.6303 REMARK 3 L33: 0.3872 L12: -0.0311 REMARK 3 L13: 0.0125 L23: -0.2717 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.0219 S13: -0.0150 REMARK 3 S21: 0.0201 S22: 0.0063 S23: -0.0267 REMARK 3 S31: -0.0167 S32: -0.0004 S33: -0.0023 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3O7N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91339 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26238 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 37.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.61600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: PDB ENTRY 2QFK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 32% W/V PEG REMARK 280 4000, PH 5.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 28.96250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.62650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.65250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.62650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.96250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.65250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 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 OE2 GLU A 65 O HOH A 236 1.92 REMARK 500 OD2 ASP A 54 O HOH A 369 2.12 REMARK 500 O ASP A 72 NH2 ARG A 122 2.14 REMARK 500 OH TYR A 38 O HOH A 340 2.15 REMARK 500 OE1 GLN A 118 O HOH A 255 2.15 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 OD2 ASP B 30 O HOH A 202 2454 2.16 REMARK 500 O1 SO4 B 197 O HOH A 204 2454 2.19 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 TRP A 59 CB TRP A 59 CG -0.114 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 68 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG B 32 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG B 32 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG B 122 NE - CZ - NH2 ANGL. DEV. = -3.0 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 72 51.51 37.62 REMARK 500 ASP B 12 53.57 -153.91 REMARK 500 ASP B 12 45.13 -150.27 REMARK 500 ASN B 37 8.01 81.57 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 GLY A 112 GLN A 113 -139.76 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 139 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 89 NE2 REMARK 620 2 HEM A 139 NA 92.0 REMARK 620 3 HEM A 139 NB 89.8 88.5 REMARK 620 4 HEM A 139 NC 93.8 173.8 89.4 REMARK 620 5 HEM A 139 ND 95.3 89.7 174.6 91.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 139 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 89 NE2 REMARK 620 2 HEM B 139 NA 94.8 REMARK 620 3 HEM B 139 NB 91.4 90.9 REMARK 620 4 HEM B 139 NC 91.6 173.5 89.1 REMARK 620 5 HEM B 139 ND 96.3 87.9 172.3 91.3 REMARK 620 N 1 2 3 4 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 139 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BML A 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 196 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 198 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 139 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BML B 192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 197 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3K3U RELATED DB: PDB REMARK 900 DEHALOPEROXIDASE V59W MUTANT STRUCTURE, NO LIGAND REMARK 900 RELATED ID: 2QFK RELATED DB: PDB REMARK 900 WILDE-TYPE DEHALOPEROXIDASE STRUCTURE IN METAQUO FORM REMARK 900 RELATED ID: 3LB2 RELATED DB: PDB REMARK 900 WILDE-TYPE DEHALOPEROXIDASE STRUCTURE IN COMPLEX WITH 4-BROMOPHENOL DBREF 3O7N A 1 137 UNP Q9NAV8 Q9NAV8_9ANNE 2 138 DBREF 3O7N B 1 137 UNP Q9NAV8 Q9NAV8_9ANNE 2 138 SEQADV 3O7N TRP A 59 UNP Q9NAV8 VAL 60 ENGINEERED MUTATION SEQADV 3O7N TRP B 59 UNP Q9NAV8 VAL 60 ENGINEERED MUTATION SEQRES 1 A 137 GLY PHE LYS GLN ASP ILE ALA THR ILE ARG GLY ASP LEU SEQRES 2 A 137 ARG THR TYR ALA GLN ASP ILE PHE LEU ALA PHE LEU ASN SEQRES 3 A 137 LYS TYR PRO ASP GLU ARG ARG TYR PHE LYS ASN TYR VAL SEQRES 4 A 137 GLY LYS SER ASP GLN GLU LEU LYS SER MET ALA LYS PHE SEQRES 5 A 137 GLY ASP HIS THR GLU LYS TRP PHE ASN LEU MET MET GLU SEQRES 6 A 137 VAL ALA ASP ARG ALA THR ASP CYS VAL PRO LEU ALA SER SEQRES 7 A 137 ASP ALA ASN THR LEU VAL GLN MET LYS GLN HIS SER SER SEQRES 8 A 137 LEU THR THR GLY ASN PHE GLU LYS LEU PHE VAL ALA LEU SEQRES 9 A 137 VAL GLU TYR MET ARG ALA SER GLY GLN SER PHE ASP SER SEQRES 10 A 137 GLN SER TRP ASP ARG PHE GLY LYS ASN LEU VAL SER ALA SEQRES 11 A 137 LEU SER SER ALA GLY MET LYS SEQRES 1 B 137 GLY PHE LYS GLN ASP ILE ALA THR ILE ARG GLY ASP LEU SEQRES 2 B 137 ARG THR TYR ALA GLN ASP ILE PHE LEU ALA PHE LEU ASN SEQRES 3 B 137 LYS TYR PRO ASP GLU ARG ARG TYR PHE LYS ASN TYR VAL SEQRES 4 B 137 GLY LYS SER ASP GLN GLU LEU LYS SER MET ALA LYS PHE SEQRES 5 B 137 GLY ASP HIS THR GLU LYS TRP PHE ASN LEU MET MET GLU SEQRES 6 B 137 VAL ALA ASP ARG ALA THR ASP CYS VAL PRO LEU ALA SER SEQRES 7 B 137 ASP ALA ASN THR LEU VAL GLN MET LYS GLN HIS SER SER SEQRES 8 B 137 LEU THR THR GLY ASN PHE GLU LYS LEU PHE VAL ALA LEU SEQRES 9 B 137 VAL GLU TYR MET ARG ALA SER GLY GLN SER PHE ASP SER SEQRES 10 B 137 GLN SER TRP ASP ARG PHE GLY LYS ASN LEU VAL SER ALA SEQRES 11 B 137 LEU SER SER ALA GLY MET LYS HET HEM A 139 46 HET BML A 191 8 HET SO4 A 196 5 HET SO4 A 198 5 HET HEM B 139 47 HET BML B 192 8 HET SO4 B 197 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM BML 4-BROMOPHENOL HETNAM SO4 SULFATE ION HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 BML 2(C6 H5 BR O) FORMUL 5 SO4 3(O4 S 2-) FORMUL 10 HOH *318(H2 O) HELIX 1 1 GLY A 1 ASP A 12 1 12 HELIX 2 2 ASP A 12 TYR A 28 1 17 HELIX 3 3 PRO A 29 VAL A 39 5 11 HELIX 4 4 SER A 42 SER A 48 1 7 HELIX 5 5 MET A 49 ALA A 70 1 22 HELIX 6 6 LEU A 76 MET A 86 1 11 HELIX 7 7 LYS A 87 SER A 90 5 4 HELIX 8 8 THR A 93 SER A 111 1 19 HELIX 9 9 ASP A 116 ALA A 134 1 19 HELIX 10 10 GLY B 1 GLY B 11 1 11 HELIX 11 11 ASP B 12 TYR B 28 1 17 HELIX 12 12 PRO B 29 PHE B 35 5 7 HELIX 13 13 SER B 42 SER B 48 1 7 HELIX 14 14 LYS B 51 ALA B 70 1 20 HELIX 15 15 LEU B 76 MET B 86 1 11 HELIX 16 16 LYS B 87 SER B 90 5 4 HELIX 17 17 THR B 93 SER B 111 1 19 HELIX 18 18 ASP B 116 ALA B 134 1 19 LINK NE2 HIS A 89 FE HEM A 139 1555 1555 2.13 LINK NE2 HIS B 89 FE HEM B 139 1555 1555 2.12 SITE 1 AC1 16 PHE A 24 GLU A 31 TYR A 34 PHE A 35 SITE 2 AC1 16 HIS A 55 LYS A 58 TRP A 59 MET A 63 SITE 3 AC1 16 MET A 86 GLN A 88 HIS A 89 LEU A 92 SITE 4 AC1 16 ASN A 96 PHE A 97 LEU A 127 HOH A 340 SITE 1 AC2 9 PHE A 21 PHE A 35 TYR A 38 PHE A 52 SITE 2 AC2 9 HIS A 55 THR A 56 TRP A 59 HOH A 200 SITE 3 AC2 9 HOH A 340 SITE 1 AC3 11 ARG A 32 VAL A 39 GLY A 40 HOH A 214 SITE 2 AC3 11 HOH A 217 HOH A 260 HOH A 359 GLY B 1 SITE 3 AC3 11 PHE B 2 LYS B 3 HOH B 224 SITE 1 AC4 9 PHE A 2 LYS A 3 HOH A 218 HOH A 271 SITE 2 AC4 9 HOH A 312 ARG B 32 VAL B 39 GLY B 40 SITE 3 AC4 9 HOH B 206 SITE 1 AC5 18 PHE B 24 GLU B 31 TYR B 34 PHE B 35 SITE 2 AC5 18 HIS B 55 LYS B 58 TRP B 59 MET B 63 SITE 3 AC5 18 MET B 86 GLN B 88 HIS B 89 LEU B 92 SITE 4 AC5 18 ASN B 96 PHE B 97 LEU B 127 HOH B 201 SITE 5 AC5 18 HOH B 247 HOH B 288 SITE 1 AC6 7 PHE B 21 PHE B 35 HIS B 55 THR B 56 SITE 2 AC6 7 PHE B 60 HOH B 200 HOH B 201 SITE 1 AC7 9 LYS A 99 HOH A 204 ASP B 30 GLU B 31 SITE 2 AC7 9 ARG B 33 TYR B 34 ASN B 96 LYS B 99 SITE 3 AC7 9 HOH B 254 CRYST1 57.925 67.305 69.253 90.00 90.00 90.00 P 21 21 21 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 0.017264 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014440 0.00000 CONECT 886 2900 CONECT 2375 2965 CONECT 2855 2859 2889 CONECT 2856 2862 2872 CONECT 2857 2875 2879 CONECT 2858 2882 2886 CONECT 2859 2855 2860 2896 CONECT 2860 2859 2861 2864 CONECT 2861 2860 2862 2863 CONECT 2862 2856 2861 2896 CONECT 2863 2861 CONECT 2864 2860 2865 2866 CONECT 2865 2864 2867 CONECT 2866 2864 2868 CONECT 2867 2865 2869 CONECT 2868 2866 2870 2871 CONECT 2869 2867 CONECT 2870 2868 CONECT 2871 2868 CONECT 2872 2856 2873 2897 CONECT 2873 2872 2874 2876 CONECT 2874 2873 2875 2877 CONECT 2875 2857 2874 2897 CONECT 2876 2873 CONECT 2877 2874 2878 CONECT 2878 2877 CONECT 2879 2857 2880 2898 CONECT 2880 2879 2881 2883 CONECT 2881 2880 2882 2884 CONECT 2882 2858 2881 2898 CONECT 2883 2880 CONECT 2884 2881 2885 CONECT 2885 2884 CONECT 2886 2858 2887 2899 CONECT 2887 2886 2888 2890 CONECT 2888 2887 2889 2891 CONECT 2889 2855 2888 2899 CONECT 2890 2887 CONECT 2891 2888 2892 CONECT 2892 2891 2893 CONECT 2893 2892 2894 2895 CONECT 2894 2893 CONECT 2895 2893 CONECT 2896 2859 2862 2900 CONECT 2897 2872 2875 2900 CONECT 2898 2879 2882 2900 CONECT 2899 2886 2889 2900 CONECT 2900 886 2896 2897 2898 CONECT 2900 2899 CONECT 2901 2902 CONECT 2902 2901 2903 2907 CONECT 2903 2902 2904 CONECT 2904 2903 2905 CONECT 2905 2904 2906 2908 CONECT 2906 2905 2907 CONECT 2907 2902 2906 CONECT 2908 2905 CONECT 2909 2910 2911 2912 2913 CONECT 2910 2909 CONECT 2911 2909 CONECT 2912 2909 CONECT 2913 2909 CONECT 2914 2915 2916 2917 2918 CONECT 2915 2914 CONECT 2916 2914 CONECT 2917 2914 CONECT 2918 2914 CONECT 2919 2923 2954 CONECT 2920 2926 2937 CONECT 2921 2940 2944 CONECT 2922 2947 2951 CONECT 2923 2919 2924 2961 CONECT 2924 2923 2925 2928 CONECT 2925 2924 2926 2927 CONECT 2926 2920 2925 2961 CONECT 2927 2925 CONECT 2928 2924 2929 2930 CONECT 2929 2928 2931 CONECT 2930 2928 2932 CONECT 2931 2929 2933 2935 CONECT 2932 2930 2934 2936 CONECT 2933 2931 CONECT 2934 2932 CONECT 2935 2931 CONECT 2936 2932 CONECT 2937 2920 2938 2962 CONECT 2938 2937 2939 2941 CONECT 2939 2938 2940 2942 CONECT 2940 2921 2939 2962 CONECT 2941 2938 CONECT 2942 2939 2943 CONECT 2943 2942 CONECT 2944 2921 2945 2963 CONECT 2945 2944 2946 2948 CONECT 2946 2945 2947 2949 CONECT 2947 2922 2946 2963 CONECT 2948 2945 CONECT 2949 2946 2950 CONECT 2950 2949 CONECT 2951 2922 2952 2964 CONECT 2952 2951 2953 2955 CONECT 2953 2952 2954 2956 CONECT 2954 2919 2953 2964 CONECT 2955 2952 CONECT 2956 2953 2957 CONECT 2957 2956 2958 CONECT 2958 2957 2959 2960 CONECT 2959 2958 CONECT 2960 2958 CONECT 2961 2923 2926 2965 CONECT 2962 2937 2940 2965 CONECT 2963 2944 2947 2965 CONECT 2964 2951 2954 2965 CONECT 2965 2375 2961 2962 2963 CONECT 2965 2964 CONECT 2966 2967 CONECT 2967 2966 2968 2972 CONECT 2968 2967 2969 CONECT 2969 2968 2970 CONECT 2970 2969 2971 2973 CONECT 2971 2970 2972 CONECT 2972 2967 2971 CONECT 2973 2970 CONECT 2974 2975 2976 2977 2978 CONECT 2975 2974 CONECT 2976 2974 CONECT 2977 2974 CONECT 2978 2974 MASTER 444 0 7 18 0 0 23 6 2631 2 128 22 END