HEADER LYASE 01-FEB-12 4DJA TITLE CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE PHRB FROM TITLE 2 AGROBACTERIUM TUMEFACIENS WITH AN FE-S CLUSTER AND A 6,7-DIMETHYL-8- TITLE 3 RIBITYLLUMAZINE ANTENNA CHROMOPHORE AT 1.45A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOTOLYASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS; SOURCE 3 ORGANISM_TAXID: 176299; SOURCE 4 STRAIN: C58; SOURCE 5 GENE: ATU4765; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-21B KEYWDS PHOTOLYASE, DNA REPAIR, LYASE, IRON-SULFUR CLUSTER, FLAVOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.SCHEERER,F.ZHANG,I.OBERPICHLER,T.LAMPARTER,N.KRAUSS REVDAT 5 03-APR-24 4DJA 1 REMARK REVDAT 4 28-FEB-24 4DJA 1 REMARK SEQADV LINK REVDAT 3 15-NOV-17 4DJA 1 REMARK REVDAT 2 15-MAY-13 4DJA 1 JRNL REVDAT 1 17-APR-13 4DJA 0 JRNL AUTH F.ZHANG,P.SCHEERER,I.OBERPICHLER,T.LAMPARTER,N.KRAUSS JRNL TITL CRYSTAL STRUCTURE OF A PROKARYOTIC (6-4) PHOTOLYASE WITH AN JRNL TITL 2 FE-S CLUSTER AND A 6,7-DIMETHYL-8-RIBITYLLUMAZINE ANTENNA JRNL TITL 3 CHROMOPHORE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 7217 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23589886 JRNL DOI 10.1073/PNAS.1302377110 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117/PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 92395 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4874 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4455 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 225 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4089 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 97 REMARK 3 SOLVENT ATOMS : 836 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.03000 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): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.339 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.011 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.517 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; 5.198 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ;30.183 ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ;12.293 ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ;17.228 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; 0.126 ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; 0.007 ; NULL 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 : 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): 18.2480 9.7198 51.4022 REMARK 3 T TENSOR REMARK 3 T11: 0.0030 T22: 0.0113 REMARK 3 T33: 0.0012 T12: -0.0035 REMARK 3 T13: 0.0003 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 0.0731 L22: 0.1977 REMARK 3 L33: 0.1088 L12: -0.0668 REMARK 3 L13: -0.0173 L23: 0.0702 REMARK 3 S TENSOR REMARK 3 S11: -0.0066 S12: -0.0095 S13: 0.0045 REMARK 3 S21: 0.0009 S22: 0.0125 S23: -0.0144 REMARK 3 S31: 0.0054 S32: 0.0029 S33: -0.0059 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: NULL REMARK 4 REMARK 4 4DJA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070399. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-11 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 : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SI-111 CRYSTAL - DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 104964 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 72.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.37700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD/MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELXCD, PHASER REMARK 200 STARTING MODEL: UNPUBLISHED STRUCTURAL DATA OF FE-EDGE SAD-PHASING REMARK 200 (WAVELENGTH:1.741) - 2ND CRYSTAL 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, 4% 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 21 21 2 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+1/2,Y+1/2,-Z 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 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 49.19400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.39300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.19400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.39300 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 180 REMARK 465 GLU A 181 REMARK 465 ASN A 182 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 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 ARG A 466 NE - CZ - NH2 ANGL. DEV. = -4.0 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 PHE A 178 69.89 -100.29 REMARK 500 LEU A 263 -128.11 43.89 REMARK 500 ASN A 329 65.47 -154.46 REMARK 500 ILE A 372 -80.82 -106.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 213 0.08 SIDE CHAIN 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 604 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 103 O REMARK 620 2 ASP A 129 OD2 106.2 REMARK 620 3 HOH A 799 O 74.6 105.6 REMARK 620 4 HOH A 825 O 134.2 106.8 66.6 REMARK 620 5 HOH A 989 O 103.6 118.0 134.4 87.8 REMARK 620 N 1 2 3 4 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 350 SG REMARK 620 2 SF4 A 603 S1 114.1 REMARK 620 3 SF4 A 603 S2 113.0 105.7 REMARK 620 4 SF4 A 603 S4 116.2 103.4 103.2 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 112.7 REMARK 620 3 SF4 A 603 S3 113.2 106.4 REMARK 620 4 SF4 A 603 S4 111.6 104.4 108.0 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 441 SG REMARK 620 2 SF4 A 603 S1 120.8 REMARK 620 3 SF4 A 603 S2 106.0 105.9 REMARK 620 4 SF4 A 603 S3 112.4 105.5 105.0 REMARK 620 N 1 2 3 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 454 SG REMARK 620 2 SF4 A 603 S1 118.7 REMARK 620 3 SF4 A 603 S3 117.2 104.9 REMARK 620 4 SF4 A 603 S4 105.6 102.6 106.3 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 NA 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 DBREF 4DJA A 1 507 UNP A9CH39 A9CH39_AGRT5 1 507 SEQADV 4DJA ALA A 508 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA ALA A 509 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA ALA A 510 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA LEU A 511 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA GLU A 512 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA HIS A 513 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA HIS A 514 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA HIS A 515 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA HIS A 516 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA HIS A 517 UNP A9CH39 EXPRESSION TAG SEQADV 4DJA 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 TYR 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 NA A 604 1 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 NA SODIUM ION 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 NA NA 1+ FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 HOH *836(H2 O) HELIX 1 1 ILE A 16 ASP A 20 5 5 HELIX 2 2 VAL A 34 TYR A 40 1 7 HELIX 3 3 HIS A 44 GLU A 65 1 22 HELIX 4 4 SER A 82 THR A 95 1 14 HELIX 5 5 GLU A 106 GLY A 115 1 10 HELIX 6 6 GLY A 115 GLY A 121 1 7 HELIX 7 7 SER A 135 ALA A 144 1 10 HELIX 8 8 THR A 150 GLY A 163 1 14 HELIX 9 9 GLY A 173 ARG A 175 5 3 HELIX 10 10 ASP A 201 PHE A 215 1 15 HELIX 11 11 THR A 230 PHE A 245 1 16 HELIX 12 12 LEU A 246 PHE A 249 5 4 HELIX 13 13 LEU A 268 ASN A 273 1 6 HELIX 14 14 ASP A 278 GLU A 292 1 15 HELIX 15 15 PRO A 296 GLY A 309 1 14 HELIX 16 16 GLY A 309 GLY A 322 1 14 HELIX 17 17 PRO A 323 SER A 328 5 6 HELIX 18 18 VAL A 339 GLY A 344 1 6 HELIX 19 19 MET A 348 ALA A 362 1 15 HELIX 20 20 HIS A 365 ILE A 372 1 8 HELIX 21 21 ILE A 372 ALA A 380 1 9 HELIX 22 22 ASP A 383 TYR A 395 1 13 HELIX 23 23 TYR A 399 GLY A 409 1 11 HELIX 24 24 SER A 427 SER A 435 1 9 HELIX 25 25 ASP A 436 CYS A 441 5 6 HELIX 26 26 CYS A 454 ASN A 467 1 14 HELIX 27 27 ASN A 467 LYS A 472 1 6 HELIX 28 28 ASN A 474 ARG A 476 5 3 HELIX 29 29 LEU A 477 ARG A 486 1 10 HELIX 30 30 SER A 488 HIS A 513 1 26 SHEET 1 A 5 ARG A 68 THR A 72 0 SHEET 2 A 5 THR A 28 CYS A 32 1 N ILE A 29 O ARG A 70 SHEET 3 A 5 GLN A 3 LEU A 6 1 N VAL A 5 O VAL A 30 SHEET 4 A 5 ARG A 98 THR A 102 1 O CYS A 100 N LEU A 4 SHEET 5 A 5 GLN A 123 ARG A 127 1 O ASP A 125 N ILE A 99 SHEET 1 B 2 MET A 166 ASN A 167 0 SHEET 2 B 2 GLN A 170 PRO A 171 -1 O GLN A 170 N ASN A 167 LINK O GLU A 103 NA NA A 604 1555 1555 2.74 LINK OD2 ASP A 129 NA NA A 604 1555 1555 2.61 LINK SG CYS A 350 FE3 SF4 A 603 1555 1555 2.31 LINK SG CYS A 438 FE1 SF4 A 603 1555 1555 2.31 LINK SG CYS A 441 FE4 SF4 A 603 1555 1555 2.31 LINK SG CYS A 454 FE2 SF4 A 603 1555 1555 2.30 LINK NA NA A 604 O HOH A 799 1555 1555 3.06 LINK NA NA A 604 O HOH A 825 1555 1555 2.70 LINK NA NA A 604 O HOH A 989 1555 1555 2.69 SITE 1 AC1 29 PHE A 249 HIS A 265 SER A 266 LEU A 267 SITE 2 AC1 29 LEU A 268 SER A 269 ASN A 273 PHE A 303 SITE 3 AC1 29 GLN A 306 ILE A 307 ARG A 311 TYR A 363 SITE 4 AC1 29 ALA A 364 HIS A 366 ARG A 369 TYR A 391 SITE 5 AC1 29 ASP A 397 ALA A 398 VAL A 402 GLU A 403 SITE 6 AC1 29 ASN A 406 HOH A 706 HOH A 731 HOH A 732 SITE 7 AC1 29 HOH A 757 HOH A 914 HOH A 918 HOH A1073 SITE 8 AC1 29 HOH A1446 SITE 1 AC2 16 LEU A 8 GLY A 9 ASP A 10 CYS A 32 SITE 2 AC2 16 GLU A 33 VAL A 34 GLU A 37 TYR A 40 SITE 3 AC2 16 HIS A 43 ILE A 51 PHE A 52 PHE A 83 SITE 4 AC2 16 GLY A 105 GLU A 106 TYR A 399 HOH A 735 SITE 1 AC3 8 MET A 348 CYS A 350 ILE A 431 TYR A 437 SITE 2 AC3 8 CYS A 438 CYS A 441 TYR A 443 CYS A 454 SITE 1 AC4 6 GLU A 103 PRO A 104 ASP A 129 HOH A 799 SITE 2 AC4 6 HOH A 825 HOH A 989 SITE 1 AC5 3 PRO A 14 GLU A 65 HOH A1315 SITE 1 AC6 2 GLU A 332 ASP A 334 CRYST1 98.388 106.786 55.913 90.00 90.00 90.00 P 21 21 2 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 0.010164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009365 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017885 0.00000