HEADER OXIDOREDUCTASE 16-JUN-16 5KIL TITLE CMLA BETA-HYDROXYLASE E377D MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CMLA PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE (STRAIN ATCC 10712 / SOURCE 3 CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745); SOURCE 4 ORGANISM_TAXID: 953739; SOURCE 5 STRAIN: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 SOURCE 6 / PD 04745; SOURCE 7 GENE: SVEN_0921; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 KEYWDS OXYGEN ACTIVATION, DIIRON CLUSTER, ANTIBIOTIC BIOSYNTHESIS, BETA- KEYWDS 2 HYDROXYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.J.KNOOT,J.D.LIPSCOMB REVDAT 4 27-SEP-23 5KIL 1 REMARK REVDAT 3 25-DEC-19 5KIL 1 REMARK REVDAT 2 20-SEP-17 5KIL 1 REMARK REVDAT 1 26-APR-17 5KIL 0 JRNL AUTH A.J.JASNIEWSKI,C.J.KNOOT,J.D.LIPSCOMB,L.QUE JRNL TITL A CARBOXYLATE SHIFT REGULATES DIOXYGEN ACTIVATION BY THE JRNL TITL 2 DIIRON NONHEME BETA-HYDROXYLASE CMLA UPON BINDING OF A JRNL TITL 3 SUBSTRATE-LOADED NONRIBOSOMAL PEPTIDE SYNTHETASE. JRNL REF BIOCHEMISTRY V. 55 5818 2016 JRNL REFN ISSN 1520-4995 JRNL PMID 27668828 JRNL DOI 10.1021/ACS.BIOCHEM.6B00834 REMARK 2 REMARK 2 RESOLUTION. 2.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 28730 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1536 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2080 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4096 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : 0.36000 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): 0.327 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.276 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.229 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.057 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4221 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5742 ; 1.969 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 7.418 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 219 ;32.451 ;22.146 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 659 ;19.372 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 51 ;22.886 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 616 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3327 ; 0.010 ; 0.021 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): 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: NULL REMARK 4 REMARK 4 5KIL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222225. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30307 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.720 REMARK 200 RESOLUTION RANGE LOW (A) : 38.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.7.0029 REMARK 200 STARTING MODEL: 4JO0 REMARK 200 REMARK 200 REMARK: SQUARE BIPYRAMIDAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20000, POTASSIUM ACETATE, HEPES, REMARK 280 GLYCEROL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 46.27400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 76.97700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 76.97700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 69.41100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 76.97700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 76.97700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 23.13700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 76.97700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 76.97700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 69.41100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 76.97700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 76.97700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 23.13700 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 46.27400 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: 7250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 -46.27400 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 ALA A 237 REMARK 465 ALA A 238 REMARK 465 SER A 239 REMARK 465 GLU A 240 REMARK 465 ALA A 241 REMARK 465 PRO A 242 REMARK 465 ALA A 243 REMARK 465 PRO A 244 REMARK 465 ALA A 245 REMARK 465 SER A 246 REMARK 465 SER A 247 REMARK 465 SER A 248 REMARK 465 GLU A 249 REMARK 465 ALA A 494 REMARK 465 VAL A 495 REMARK 465 ASP A 496 REMARK 465 TYR A 497 REMARK 465 ASP A 498 REMARK 465 GLU A 499 REMARK 465 SER A 500 REMARK 465 HIS A 501 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 O ILE A 383 NZ LYS A 386 2.06 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 157 CB TRP A 157 CG 0.116 REMARK 500 GLU A 250 CD GLU A 250 OE1 0.145 REMARK 500 GLU A 250 CD GLU A 250 OE2 0.167 REMARK 500 GLU A 250 C GLU A 250 O 0.208 REMARK 500 ALA A 334 C ALA A 334 O 0.121 REMARK 500 SER A 335 CB SER A 335 OG 0.078 REMARK 500 ILE A 383 C ILE A 383 O 0.122 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 TRP A 157 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 ASP A 352 CB - CG - OD1 ANGL. DEV. = 5.4 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 ARG A 36 -68.02 -138.88 REMARK 500 ALA A 68 70.87 -115.22 REMARK 500 CYS A 111 139.19 -35.55 REMARK 500 PRO A 114 -9.24 -58.39 REMARK 500 ASN A 135 -1.72 66.68 REMARK 500 VAL A 256 -0.53 -147.85 REMARK 500 HIS A 258 -95.60 47.71 REMARK 500 ASN A 287 11.44 87.06 REMARK 500 MET A 311 82.34 -164.06 REMARK 500 ARG A 320 -53.94 -29.42 REMARK 500 ASP A 338 87.35 -151.86 REMARK 500 LEU A 359 17.73 58.16 REMARK 500 ASP A 377 3.48 84.12 REMARK 500 SER A 385 70.38 -69.48 REMARK 500 ALA A 402 -142.02 45.32 REMARK 500 GLU A 430 58.42 -58.86 REMARK 500 GLU A 474 75.08 38.51 REMARK 500 TYR A 481 -153.81 -127.81 REMARK 500 GLU A 522 135.24 173.03 REMARK 500 LEU A 526 -59.17 75.35 REMARK 500 ARG A 528 122.64 -176.36 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 K A 602 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 148 O REMARK 620 2 SER A 150 O 88.5 REMARK 620 3 TYR A 153 O 104.9 71.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FEO A 601 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 305 NE2 REMARK 620 2 FEO A 601 O 93.2 REMARK 620 3 HIS A 307 ND1 87.2 77.5 REMARK 620 4 ASP A 377 OD2 102.1 163.8 98.0 REMARK 620 5 ASP A 403 OD2 81.4 77.5 151.8 109.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FEO A 601 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 309 OD2 REMARK 620 2 FEO A 601 O 90.0 REMARK 620 3 HIS A 310 NE2 102.4 94.6 REMARK 620 4 ASP A 403 OD2 151.3 61.3 79.8 REMARK 620 5 ACT A 603 O 92.1 86.4 165.4 88.1 REMARK 620 6 ACT A 603 OXT 113.3 138.9 111.5 91.7 60.5 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 FEO A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 603 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JO0 RELATED DB: PDB REMARK 900 4JO0 IS THE WT ENZYME IN OXIDIZED CLUSTER STATE REMARK 900 RELATED ID: 5KIK RELATED DB: PDB REMARK 900 WT ENZYME IN THE CHEMICALLY REDUCED STATE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONFLICT AT POSITION 190 IS LIKELY DUE TO AN ERROR IN THE REMARK 999 GENOME SEQUENCE OF THE SVEN_0921 GENE FROM STREPTOMYCES VENEZUELAE DBREF 5KIL A 0 532 UNP F2RB80 F2RB80_STRVP 1 532 SEQADV 5KIL MET A -19 UNP F2RB80 INITIATING METHIONINE SEQADV 5KIL GLY A -18 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL SER A -17 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL SER A -16 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL HIS A -15 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL HIS A -14 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL HIS A -13 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL HIS A -12 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL HIS A -11 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL SER A -10 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL SER A -9 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL GLY A -8 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL LEU A -7 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL VAL A -6 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL PRO A -5 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL ARG A -4 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL GLY A -3 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL SER A -2 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL HIS A -1 UNP F2RB80 EXPRESSION TAG SEQADV 5KIL ASN A 189 UNP F2RB80 ASP 190 SEE REMARK 999 SEQADV 5KIL ASP A 377 UNP F2RB80 GLU 377 ENGINEERED MUTATION SEQRES 1 A 551 MET GLY SER SER HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 551 VAL PRO ARG GLY SER HIS MET ARG TYR SER LEU ARG GLN SEQRES 3 A 551 ASP ILE ALA VAL GLU PRO VAL ILE ALA GLY TRP TYR GLY SEQRES 4 A 551 TRP SER TYR LEU LEU PRO PRO GLN THR LEU ALA ARG PHE SEQRES 5 A 551 VAL HIS ASN ARG PHE ASN ARG ILE VAL GLU SER TYR LEU SEQRES 6 A 551 ASP ASP PRO GLN VAL HIS ALA ALA ALA VAL ARG GLN ARG SEQRES 7 A 551 ARG MET HIS GLY GLY PRO TRP ILE HIS ALA HIS GLU HIS SEQRES 8 A 551 ARG ASP ALA ILE GLU ALA TRP TYR ARG GLU THR ALA PRO SEQRES 9 A 551 ARG ARG GLU ARG LEU ASP GLU LEU PHE GLU ALA VAL ARG SEQRES 10 A 551 ARG LEU GLU GLU ASP ILE LEU PRO ARG HIS HIS GLY GLU SEQRES 11 A 551 CYS LEU ASP PRO VAL TYR GLN GLU LEU PRO ALA ALA LEU SEQRES 12 A 551 ALA GLY ARG VAL GLU VAL PHE TYR GLY ARG ASP ASN ARG SEQRES 13 A 551 THR ALA ASP TYR ARG PHE VAL GLU PRO LEU MET TYR ALA SEQRES 14 A 551 SER GLU TYR TYR ASP GLU SER TRP GLN GLN VAL ARG PHE SEQRES 15 A 551 ARG PRO VAL THR GLU ASP ALA ARG GLU PHE ALA LEU THR SEQRES 16 A 551 THR PRO MET LEU GLU TYR GLY PRO GLU GLN LEU LEU VAL SEQRES 17 A 551 ASN VAL PRO LEU ASN SER PRO LEU LEU ASP ALA VAL PHE SEQRES 18 A 551 ARG GLY GLY LEU THR GLY THR GLU LEU ASP ASP LEU ALA SEQRES 19 A 551 ALA ARG PHE GLY LEU ASP GLY GLU ARG ALA ALA ARG PHE SEQRES 20 A 551 ALA SER TYR PHE GLU PRO THR PRO ALA ALA SER GLU ALA SEQRES 21 A 551 PRO ALA PRO ALA SER SER SER GLU GLU ASP VAL LEU GLU SEQRES 22 A 551 TYR VAL GLY HIS ALA CYS VAL PHE ALA ARG HIS ARG GLY SEQRES 23 A 551 THR THR PHE LEU VAL ASP PRO VAL LEU SER TYR SER GLY SEQRES 24 A 551 TYR PRO GLY GLY ALA GLU ASN ARG PHE THR PHE ALA ASP SEQRES 25 A 551 LEU PRO GLU ARG ILE ASP HIS LEU LEU ILE THR HIS ASN SEQRES 26 A 551 HIS GLN ASP HIS MET LEU PHE GLU THR LEU LEU ARG ILE SEQRES 27 A 551 ARG HIS ARG VAL GLY ARG VAL LEU VAL PRO LYS SER THR SEQRES 28 A 551 ASN ALA SER LEU VAL ASP PRO GLY LEU GLY GLY ILE LEU SEQRES 29 A 551 ARG ARG LEU GLY PHE THR ASP VAL VAL GLU VAL ASP ASP SEQRES 30 A 551 LEU GLU THR LEU SER CYS GLY SER ALA GLU VAL VAL ALA SEQRES 31 A 551 LEU PRO PHE LEU GLY ASP HIS GLY ASP LEU ARG ILE ARG SEQRES 32 A 551 SER LYS THR GLY TRP LEU ILE ARG PHE GLY GLU ARG SER SEQRES 33 A 551 VAL LEU PHE ALA ALA ASP SER THR ASN ILE SER PRO THR SEQRES 34 A 551 MET TYR THR LYS VAL ALA GLU VAL ILE GLY PRO VAL ASP SEQRES 35 A 551 THR VAL PHE ILE GLY MET GLU SER ILE GLY ALA ALA ALA SEQRES 36 A 551 SER TRP ILE TYR GLY PRO LEU TYR GLY GLU PRO LEU ASP SEQRES 37 A 551 ARG ARG THR ASP GLN SER ARG ARG LEU ASN GLY SER ASN SEQRES 38 A 551 PHE PRO GLN ALA ARG GLU ILE VAL ASP ALA LEU GLU PRO SEQRES 39 A 551 ASP GLU VAL TYR VAL TYR ALA MET GLY LEU GLU PRO TRP SEQRES 40 A 551 MET GLY VAL VAL MET ALA VAL ASP TYR ASP GLU SER HIS SEQRES 41 A 551 PRO ALA ILE VAL ASP SER ASP LEU LEU VAL ARG HIS VAL SEQRES 42 A 551 GLN ASP LYS GLY GLY THR ALA GLU ARG LEU HIS LEU ARG SEQRES 43 A 551 ARG THR LEU ARG LEU HET FEO A 601 3 HET K A 602 1 HET ACT A 603 4 HETNAM FEO MU-OXO-DIIRON HETNAM K POTASSIUM ION HETNAM ACT ACETATE ION FORMUL 2 FEO FE2 O FORMUL 3 K K 1+ FORMUL 4 ACT C2 H3 O2 1- FORMUL 5 HOH *19(H2 O) HELIX 1 AA1 TRP A 20 LEU A 24 5 5 HELIX 2 AA2 PRO A 25 ARG A 36 1 12 HELIX 3 AA3 ARG A 36 ASP A 47 1 12 HELIX 4 AA4 ASP A 47 GLN A 57 1 11 HELIX 5 AA5 ARG A 58 HIS A 61 5 4 HELIX 6 AA6 ALA A 68 GLU A 70 5 3 HELIX 7 AA7 HIS A 71 THR A 82 1 12 HELIX 8 AA8 THR A 82 ASP A 102 1 21 HELIX 9 AA9 ILE A 103 HIS A 107 5 5 HELIX 10 AB1 LEU A 112 TYR A 116 5 5 HELIX 11 AB2 VAL A 143 ALA A 149 1 7 HELIX 12 AB3 ASP A 154 SER A 156 5 3 HELIX 13 AB4 SER A 194 GLY A 203 1 10 HELIX 14 AB5 THR A 206 PHE A 217 1 12 HELIX 15 AB6 ASP A 220 SER A 229 1 10 HELIX 16 AB7 THR A 290 LEU A 294 5 5 HELIX 17 AB8 HIS A 307 MET A 311 5 5 HELIX 18 AB9 LEU A 312 ARG A 320 1 9 HELIX 19 AC1 GLY A 340 LEU A 348 1 9 HELIX 20 AC2 THR A 410 GLY A 420 1 11 HELIX 21 AC3 ALA A 435 ILE A 439 5 5 HELIX 22 AC4 TYR A 440 TYR A 444 5 5 HELIX 23 AC5 ASP A 449 ARG A 456 1 8 HELIX 24 AC6 ASN A 462 GLU A 474 1 13 HELIX 25 AC7 GLU A 486 VAL A 492 5 7 HELIX 26 AC8 ALA A 503 LYS A 517 1 15 SHEET 1 AA1 2 TYR A 2 LEU A 4 0 SHEET 2 AA1 2 PHE A 231 PRO A 233 -1 O GLU A 232 N SER A 3 SHEET 1 AA2 4 TRP A 17 TYR A 18 0 SHEET 2 AA2 4 ILE A 8 ILE A 14 -1 N ILE A 14 O TRP A 17 SHEET 3 AA2 4 GLN A 158 PRO A 164 -1 O ARG A 163 N ALA A 9 SHEET 4 AA2 4 LEU A 186 ASN A 189 -1 O VAL A 188 N VAL A 160 SHEET 1 AA3 2 VAL A 127 TYR A 131 0 SHEET 2 AA3 2 ALA A 138 PHE A 142 -1 O ASP A 139 N PHE A 130 SHEET 1 AA4 7 VAL A 353 VAL A 356 0 SHEET 2 AA4 7 VAL A 323 PRO A 329 1 N VAL A 326 O VAL A 354 SHEET 3 AA4 7 ILE A 298 LEU A 302 1 N ILE A 298 O GLY A 324 SHEET 4 AA4 7 THR A 268 VAL A 272 1 N LEU A 271 O LEU A 302 SHEET 5 AA4 7 CYS A 260 HIS A 265 -1 N ALA A 263 O PHE A 270 SHEET 6 AA4 7 VAL A 252 GLY A 257 -1 N GLY A 257 O CYS A 260 SHEET 7 AA4 7 ARG A 528 LEU A 530 -1 O ARG A 528 N TYR A 255 SHEET 1 AA5 7 THR A 361 CYS A 364 0 SHEET 2 AA5 7 ALA A 367 LEU A 372 -1 O VAL A 369 N LEU A 362 SHEET 3 AA5 7 GLY A 388 PHE A 393 -1 O ARG A 392 N GLU A 368 SHEET 4 AA5 7 ARG A 396 PHE A 400 -1 O VAL A 398 N ILE A 391 SHEET 5 AA5 7 THR A 424 GLY A 428 1 O THR A 424 N LEU A 399 SHEET 6 AA5 7 GLU A 477 TYR A 481 1 O TYR A 479 N VAL A 425 SHEET 7 AA5 7 THR A 520 ARG A 523 1 O GLU A 522 N VAL A 480 LINK O TYR A 148 K K A 602 1555 1555 2.71 LINK O SER A 150 K K A 602 1555 1555 2.81 LINK O TYR A 153 K K A 602 1555 1555 2.83 LINK NE2 HIS A 305 FE1 FEO A 601 1555 1555 2.36 LINK ND1 HIS A 307 FE1 FEO A 601 1555 1555 2.03 LINK OD2 ASP A 309 FE2 FEO A 601 1555 1555 1.85 LINK NE2 HIS A 310 FE2 FEO A 601 1555 1555 2.40 LINK OD2 ASP A 377 FE1 FEO A 601 1555 1555 1.86 LINK OD2 ASP A 403 FE2 FEO A 601 1555 1555 2.45 LINK OD2 ASP A 403 FE1 FEO A 601 1555 1555 2.08 LINK FE2 FEO A 601 O ACT A 603 1555 1555 2.30 LINK FE2 FEO A 601 OXT ACT A 603 1555 1555 2.15 SITE 1 AC1 7 HIS A 305 HIS A 307 ASP A 309 HIS A 310 SITE 2 AC1 7 ASP A 377 ASP A 403 ACT A 603 SITE 1 AC2 3 TYR A 148 SER A 150 TYR A 153 SITE 1 AC3 6 HIS A 258 ASP A 309 ASP A 403 GLU A 430 SITE 2 AC3 6 ALA A 482 FEO A 601 CRYST1 153.954 153.954 92.548 90.00 90.00 90.00 P 43 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 0.006495 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006495 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010805 0.00000