HEADER LYASE 30-JUN-16 5LFA TITLE CRYSTAL STRUCTURE OF IRON-SULFUR CLUSTER CONTAINING BACTERIAL (6-4) TITLE 2 PHOTOLYASE PHRB - Y424F MUTANT WITH IMPAIRED DNA REPAIR ACTIVITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: (6-4) PHOTOLYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: (6-4)DNA PHOTOLYASE,DNA PHOTOLYASE PHRB,PHOTOREACTIVATING COMPND 5 ENZYME PHRB; COMPND 6 EC: 4.1.99.13; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 OTHER_DETAILS: Y424F MUTANT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM FABRUM (STRAIN C58 / ATCC 33970); SOURCE 3 ORGANISM_TAXID: 176299; SOURCE 4 GENE: PHRB, ATU4765; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21B KEYWDS PHOTOLYASE, DNA REPAIR, LYASE, IRON-SULFUR CLUSTER, FLAVOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.KWIATKOWSKI,F.ZHANG,N.KRAUSS,T.LAMPARTER,P.SCHEERER REVDAT 3 10-JAN-24 5LFA 1 REMARK REVDAT 2 01-MAR-17 5LFA 1 JRNL REVDAT 1 11-JAN-17 5LFA 0 JRNL AUTH F.ZHANG,H.MA,K.BOWATTE,D.KWIATKOWSKI,E.MITTMANN,H.QASEM, JRNL AUTH 2 N.KRAU,X.ZENG,Z.REN,P.SCHEERER,X.YANG,T.LAMPARTER JRNL TITL CRYSTAL STRUCTURES OF BACTERIAL (6-4) PHOTOLYASE MUTANTS JRNL TITL 2 WITH IMPAIRED DNA REPAIR ACTIVITY. JRNL REF PHOTOCHEM. PHOTOBIOL. V. 93 304 2017 JRNL REFN ISSN 1751-1097 JRNL PMID 27992645 JRNL DOI 10.1111/PHP.12699 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 69.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18586 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1031 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1365 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3916 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.71000 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): 0.288 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.232 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.531 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4138 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3720 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5622 ; 1.303 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8497 ; 0.970 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 502 ; 5.039 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;29.245 ;22.941 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 618 ;13.122 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;15.551 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 589 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4732 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1035 ; 0.001 ; 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): 2002 ; 1.935 ; 2.774 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2001 ; 1.928 ; 2.773 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2500 ; 2.711 ; 4.156 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2501 ; 2.711 ; 4.157 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2136 ; 1.920 ; 2.855 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2136 ; 1.919 ; 2.855 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3109 ; 2.532 ; 4.224 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 17791 ; 3.538 ;50.829 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 17791 ; 3.539 ;50.828 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 7856 ; 2.346 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 31 ;32.756 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7827 ;13.222 ; 5.000 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 : 1 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 2 A 513 REMARK 3 ORIGIN FOR THE GROUP (A): -3.9430 -30.1150 11.0990 REMARK 3 T TENSOR REMARK 3 T11: 0.0041 T22: 0.0034 REMARK 3 T33: 0.0540 T12: -0.0025 REMARK 3 T13: -0.0012 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 0.1085 L22: 0.0381 REMARK 3 L33: 0.1409 L12: -0.0143 REMARK 3 L13: 0.0762 L23: -0.0495 REMARK 3 S TENSOR REMARK 3 S11: -0.0015 S12: 0.0095 S13: -0.0084 REMARK 3 S21: 0.0113 S22: -0.0101 S23: 0.0063 REMARK 3 S31: -0.0186 S32: 0.0139 S33: 0.0116 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5LFA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1200000557. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96863 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS BUILT=20160514 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19657 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 69.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.20000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.75000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 4DJA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES, 5% PEG400, PH 6.0,, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.22050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.78950 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.22050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 51.78950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 801 LIES ON A SPECIAL POSITION. 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 ALA A 180 REMARK 465 GLU A 181 REMARK 465 ASN A 182 REMARK 465 ARG A 183 REMARK 465 GLN A 184 REMARK 465 PRO A 185 REMARK 465 ALA A 186 REMARK 465 ARG A 187 REMARK 465 PRO A 188 REMARK 465 ASP A 189 REMARK 465 LEU A 190 REMARK 465 LEU A 191 REMARK 465 HIS A 514 REMARK 465 HIS A 515 REMARK 465 HIS A 516 REMARK 465 HIS A 517 REMARK 465 HIS A 518 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 VAL A 87 CG1 CG2 REMARK 470 LYS A 88 CG CD CE NZ REMARK 470 ILE A 91 CG1 CG2 CD1 REMARK 470 THR A 95 OG1 CG2 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 GLU A 152 CG CD OE1 OE2 REMARK 470 ASN A 167 CG OD1 ND2 REMARK 470 ARG A 175 CG CD NE CZ NH1 NH2 REMARK 470 PHE A 178 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 179 CG OD1 OD2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 GLN A 253 CG CD OE1 NE2 REMARK 470 ASP A 259 CG OD1 OD2 REMARK 470 VAL A 339 CG1 CG2 REMARK 470 LYS A 345 CG CD CE NZ REMARK 470 LYS A 353 CG CD CE NZ REMARK 470 LYS A 422 CG CD CE NZ REMARK 470 GLU A 447 CG CD OE1 OE2 REMARK 470 ARG A 468 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 475 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 476 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 479 CG CD OE1 NE2 REMARK 470 LEU A 511 CG CD1 CD2 REMARK 470 GLU A 512 CG CD OE1 OE2 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 LEU A 12 59.07 -90.65 REMARK 500 THR A 95 55.60 39.35 REMARK 500 ARG A 130 2.13 -67.27 REMARK 500 ASN A 167 70.19 -102.89 REMARK 500 PHE A 178 41.47 -156.72 REMARK 500 LEU A 263 -129.01 55.87 REMARK 500 ASN A 329 69.61 -154.31 REMARK 500 ILE A 372 -81.95 -106.13 REMARK 500 PHE A 424 43.77 -98.59 REMARK 500 GLU A 512 105.70 -57.86 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 SF4 A 603 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 350 SG REMARK 620 2 SF4 A 603 S1 125.4 REMARK 620 3 SF4 A 603 S3 132.0 88.7 REMARK 620 4 SF4 A 603 S4 119.1 87.1 92.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 603 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 438 SG REMARK 620 2 SF4 A 603 S2 119.0 REMARK 620 3 SF4 A 603 S3 124.7 91.0 REMARK 620 4 SF4 A 603 S4 128.8 90.8 92.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 603 FE3 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 441 SG REMARK 620 2 SF4 A 603 S1 127.0 REMARK 620 3 SF4 A 603 S2 133.9 87.9 REMARK 620 4 SF4 A 603 S4 117.8 85.9 90.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SF4 A 603 FE4 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 454 SG REMARK 620 2 SF4 A 603 S1 132.3 REMARK 620 3 SF4 A 603 S2 128.4 88.0 REMARK 620 4 SF4 A 603 S3 116.5 88.7 90.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DLZ A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SF4 A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 606 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DJA RELATED DB: PDB REMARK 900 4DJA CONTAINS THE WILDTYP STRUCTURE DBREF 5LFA A 1 507 UNP A9CH39 PHRB_AGRFC 1 507 SEQADV 5LFA PHE A 424 UNP A9CH39 TYR 424 ENGINEERED MUTATION SEQADV 5LFA ALA A 508 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA ALA A 509 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA ALA A 510 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA LEU A 511 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA GLU A 512 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA HIS A 513 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA HIS A 514 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA HIS A 515 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA HIS A 516 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA HIS A 517 UNP A9CH39 EXPRESSION TAG SEQADV 5LFA HIS A 518 UNP A9CH39 EXPRESSION TAG SEQRES 1 A 518 MET SER GLN LEU VAL LEU ILE LEU GLY ASP GLN LEU SER SEQRES 2 A 518 PRO SER ILE ALA ALA LEU ASP GLY VAL ASP LYS LYS GLN SEQRES 3 A 518 ASP THR ILE VAL LEU CYS GLU VAL MET ALA GLU ALA SER SEQRES 4 A 518 TYR VAL GLY HIS HIS LYS LYS LYS ILE ALA PHE ILE PHE SEQRES 5 A 518 SER ALA MET ARG HIS PHE ALA GLU GLU LEU ARG GLY GLU SEQRES 6 A 518 GLY TYR ARG VAL ARG TYR THR ARG ILE ASP ASP ALA ASP SEQRES 7 A 518 ASN ALA GLY SER PHE THR GLY GLU VAL LYS ARG ALA ILE SEQRES 8 A 518 ASP ASP LEU THR PRO SER ARG ILE CYS VAL THR GLU PRO SEQRES 9 A 518 GLY GLU TRP ARG VAL ARG SER GLU MET ASP GLY PHE ALA SEQRES 10 A 518 GLY ALA PHE GLY ILE GLN VAL ASP ILE ARG SER ASP ARG SEQRES 11 A 518 ARG PHE LEU SER SER HIS GLY GLU PHE ARG ASN TRP ALA SEQRES 12 A 518 ALA GLY ARG LYS SER LEU THR MET GLU TYR PHE TYR ARG SEQRES 13 A 518 GLU MET ARG ARG LYS THR GLY LEU LEU MET ASN GLY GLU SEQRES 14 A 518 GLN PRO VAL GLY GLY ARG TRP ASN PHE ASP ALA GLU ASN SEQRES 15 A 518 ARG GLN PRO ALA ARG PRO ASP LEU LEU ARG PRO LYS HIS SEQRES 16 A 518 PRO VAL PHE ALA PRO ASP LYS ILE THR LYS GLU VAL ILE SEQRES 17 A 518 ASP THR VAL GLU ARG LEU PHE PRO ASP ASN PHE GLY LYS SEQRES 18 A 518 LEU GLU ASN PHE GLY PHE ALA VAL THR ARG THR ASP ALA SEQRES 19 A 518 GLU ARG ALA LEU SER ALA PHE ILE ASP ASP PHE LEU CYS SEQRES 20 A 518 ASN PHE GLY ALA THR GLN ASP ALA MET LEU GLN ASP ASP SEQRES 21 A 518 PRO ASN LEU ASN HIS SER LEU LEU SER PHE TYR ILE ASN SEQRES 22 A 518 CYS GLY LEU LEU ASP ALA LEU ASP VAL CYS LYS ALA ALA SEQRES 23 A 518 GLU ARG ALA TYR HIS GLU GLY GLY ALA PRO LEU ASN ALA SEQRES 24 A 518 VAL GLU GLY PHE ILE ARG GLN ILE ILE GLY TRP ARG GLU SEQRES 25 A 518 TYR MET ARG GLY ILE TYR TRP LEU ALA GLY PRO ASP TYR SEQRES 26 A 518 VAL ASP SER ASN PHE PHE GLU ASN ASP ARG SER LEU PRO SEQRES 27 A 518 VAL PHE TYR TRP THR GLY LYS THR HIS MET ASN CYS MET SEQRES 28 A 518 ALA LYS VAL ILE THR GLU THR ILE GLU ASN ALA TYR ALA SEQRES 29 A 518 HIS HIS ILE GLN ARG LEU MET ILE THR GLY ASN PHE ALA SEQRES 30 A 518 LEU LEU ALA GLY ILE ASP PRO LYS ALA VAL HIS ARG TRP SEQRES 31 A 518 TYR LEU GLU VAL TYR ALA ASP ALA TYR GLU TRP VAL GLU SEQRES 32 A 518 LEU PRO ASN VAL ILE GLY MET SER GLN PHE ALA ASP GLY SEQRES 33 A 518 GLY PHE LEU GLY THR LYS PRO PHE ALA ALA SER GLY ASN SEQRES 34 A 518 TYR ILE ASN ARG MET SER ASP TYR CYS ASP THR CYS ARG SEQRES 35 A 518 TYR ASP PRO LYS GLU ARG LEU GLY ASP ASN ALA CYS PRO SEQRES 36 A 518 PHE ASN ALA LEU TYR TRP ASP PHE LEU ALA ARG ASN ARG SEQRES 37 A 518 GLU LYS LEU LYS SER ASN HIS ARG LEU ALA GLN PRO TYR SEQRES 38 A 518 ALA THR TRP ALA ARG MET SER GLU ASP VAL ARG HIS ASP SEQRES 39 A 518 LEU ARG ALA LYS ALA ALA ALA PHE LEU ARG LYS LEU ASP SEQRES 40 A 518 ALA ALA ALA LEU GLU HIS HIS HIS HIS HIS HIS HET FAD A 601 53 HET DLZ A 602 23 HET SF4 A 603 8 HET GOL A 604 6 HET GOL A 605 6 HET GOL A 606 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM DLZ 1-DEOXY-1-(6,7-DIMETHYL-2,4-DIOXO-3,4-DIHYDROPTERIDIN- HETNAM 2 DLZ 8(2H)-YL)-D-RIBITOL HETNAM SF4 IRON/SULFUR CLUSTER HETNAM GOL GLYCEROL HETSYN DLZ 6,7-DIMETHYL-8-(1'-D-RIBITYL) LUMAZINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 DLZ C13 H18 N4 O6 FORMUL 4 SF4 FE4 S4 FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 HOH *111(H2 O) HELIX 1 AA1 ILE A 16 ASP A 20 5 5 HELIX 2 AA2 VAL A 34 TYR A 40 1 7 HELIX 3 AA3 HIS A 44 GLU A 65 1 22 HELIX 4 AA4 SER A 82 THR A 95 1 14 HELIX 5 AA5 GLU A 106 GLY A 115 1 10 HELIX 6 AA6 GLY A 115 GLY A 121 1 7 HELIX 7 AA7 SER A 135 ALA A 144 1 10 HELIX 8 AA8 THR A 150 GLY A 163 1 14 HELIX 9 AA9 GLY A 173 ARG A 175 5 3 HELIX 10 AB1 ASP A 201 PHE A 215 1 15 HELIX 11 AB2 THR A 230 PHE A 245 1 16 HELIX 12 AB3 LEU A 246 GLN A 253 5 8 HELIX 13 AB4 LEU A 268 ASN A 273 1 6 HELIX 14 AB5 ASP A 278 GLU A 292 1 15 HELIX 15 AB6 PRO A 296 GLY A 309 1 14 HELIX 16 AB7 GLY A 309 GLY A 322 1 14 HELIX 17 AB8 PRO A 323 SER A 328 5 6 HELIX 18 AB9 VAL A 339 GLY A 344 1 6 HELIX 19 AC1 MET A 348 ALA A 362 1 15 HELIX 20 AC2 HIS A 365 ILE A 372 1 8 HELIX 21 AC3 ILE A 372 ALA A 380 1 9 HELIX 22 AC4 ASP A 383 TYR A 395 1 13 HELIX 23 AC5 TYR A 399 GLY A 409 1 11 HELIX 24 AC6 SER A 427 SER A 435 1 9 HELIX 25 AC7 TYR A 437 CYS A 441 5 5 HELIX 26 AC8 CYS A 454 ASN A 467 1 14 HELIX 27 AC9 ASN A 467 LYS A 472 1 6 HELIX 28 AD1 ASN A 474 ARG A 476 5 3 HELIX 29 AD2 LEU A 477 ARG A 486 1 10 HELIX 30 AD3 SER A 488 GLU A 512 1 25 SHEET 1 AA1 5 ARG A 68 THR A 72 0 SHEET 2 AA1 5 THR A 28 CYS A 32 1 N ILE A 29 O ARG A 70 SHEET 3 AA1 5 GLN A 3 LEU A 6 1 N VAL A 5 O VAL A 30 SHEET 4 AA1 5 ARG A 98 THR A 102 1 O CYS A 100 N LEU A 4 SHEET 5 AA1 5 VAL A 124 ARG A 127 1 O ASP A 125 N ILE A 99 SHEET 1 AA2 2 MET A 166 ASN A 167 0 SHEET 2 AA2 2 GLN A 170 PRO A 171 -1 O GLN A 170 N ASN A 167 LINK SG CYS A 350 FE2 SF4 A 603 1555 1555 2.27 LINK SG CYS A 438 FE1 SF4 A 603 1555 1555 2.26 LINK SG CYS A 441 FE3 SF4 A 603 1555 1555 2.26 LINK SG CYS A 454 FE4 SF4 A 603 1555 1555 2.29 SITE 1 AC1 27 PHE A 249 HIS A 265 SER A 266 LEU A 267 SITE 2 AC1 27 LEU A 268 SER A 269 ASN A 273 PHE A 303 SITE 3 AC1 27 GLN A 306 ILE A 307 ARG A 311 TYR A 363 SITE 4 AC1 27 ALA A 364 HIS A 365 HIS A 366 ARG A 369 SITE 5 AC1 27 LEU A 370 TYR A 391 ASP A 397 ALA A 398 SITE 6 AC1 27 VAL A 402 GLU A 403 ASN A 406 VAL A 407 SITE 7 AC1 27 HOH A 718 HOH A 720 HOH A 747 SITE 1 AC2 19 LEU A 8 GLY A 9 ASP A 10 CYS A 32 SITE 2 AC2 19 GLU A 33 VAL A 34 GLU A 37 ALA A 38 SITE 3 AC2 19 TYR A 40 HIS A 43 ILE A 51 PHE A 52 SITE 4 AC2 19 MET A 55 PHE A 83 PRO A 104 GLY A 105 SITE 5 AC2 19 GLU A 106 TYR A 399 HOH A 711 SITE 1 AC3 5 CYS A 350 ILE A 431 CYS A 438 CYS A 441 SITE 2 AC3 5 CYS A 454 SITE 1 AC4 3 THR A 346 HIS A 347 TYR A 443 SITE 1 AC5 4 ARG A 56 GLU A 60 ARG A 63 TYR A 71 SITE 1 AC6 4 ARG A 192 LYS A 194 HOH A 774 HOH A 784 CRYST1 56.183 94.441 103.579 90.00 90.00 90.00 P 2 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017799 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010589 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009654 0.00000