HEADER LYASE/DNA 14-AUG-09 2WQ6 TITLE STRUCTURE OF THE 6-4 PHOTOLYASE OF D. MELANOGASTER IN COMPLEX WITH THE TITLE 2 NON-NATURAL N4-METHYL T(DEWAR)C LESION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RE11660P; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-520; COMPND 5 SYNONYM: 6-4 DNA PHOTOLYASE; COMPND 6 EC: 4.1.99.3; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*AP*CP*AP*GP*CP*GP*GP*TDYP*CDWP*GP* CP*AP*AP*GP*T)-3'; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*TP*AP*CP*CP*TP*GP*CP*GP*AP*CP* CP*GP*CP*TP*G)-3'; COMPND 14 CHAIN: D; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_TAXID: 7227; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI PLYSS (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDEST007 DERIVATIVE; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES KEYWDS LYASE-DNA COMPLEX, DNA REPAIR, DNA LESION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.F.GLAS,E.KAYA,S.SCHNEIDER,M.J.MAUL,T.CARELL REVDAT 5 20-DEC-23 2WQ6 1 REMARK REVDAT 4 08-MAY-19 2WQ6 1 REMARK LINK REVDAT 3 09-NOV-11 2WQ6 1 JRNL REMARK VERSN REVDAT 2 02-MAR-10 2WQ6 1 JRNL REVDAT 1 23-FEB-10 2WQ6 0 JRNL AUTH A.F.GLAS,E.KAYA,S.SCHNEIDER,K.HEIL,D.FAZIO,M.J.MAUL,T.CARELL JRNL TITL DNA (6-4) PHOTOLYASES REDUCE DEWAR ISOMERS FOR ISOMERIZATION JRNL TITL 2 INTO (6-4) LESIONS JRNL REF J.AM.CHEM.SOC. V. 132 3254 2010 JRNL REFN ISSN 0002-7863 JRNL PMID 20166732 JRNL DOI 10.1021/JA910917F REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 30688 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1620 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2236 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.53 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4162 REMARK 3 NUCLEIC ACID ATOMS : 609 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.88000 REMARK 3 B33 (A**2) : -0.90000 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): 0.323 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.078 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5039 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3333 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6976 ; 1.220 ; 2.128 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8067 ; 0.933 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 4.998 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 209 ;32.493 ;23.014 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 737 ;13.928 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;15.619 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 730 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5081 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 982 ; 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): 2552 ; 1.041 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1010 ; 0.221 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4136 ; 1.959 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2487 ; 2.685 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2836 ; 4.127 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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. U VALUES REFINED INDIVIDUALLY. RESIDUES DT 8 AND DC 9 REMARK 3 HAVE FORMED THE DEWAR VALENCE ISOMER OF THE 6-4 PHOTOPRODUCT BY REMARK 3 AND ARE COVALENTLY BONDED BETWEEN ATOM C6 TDY AND ATOM C4 OF CDW REMARK 4 REMARK 4 2WQ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1290040758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32351 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 43.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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 3CVU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, PH 7, 13-17% PEG1500, REMARK 280 18C, TEMPERATURE 291K 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 44.58450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.92800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.74300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.92800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.58450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.74300 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, D 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 -22 REMARK 465 ALA A -21 REMARK 465 SER A -20 REMARK 465 TRP A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 PRO A -16 REMARK 465 GLN A -15 REMARK 465 PHE A -14 REMARK 465 GLU A -13 REMARK 465 LYS A -12 REMARK 465 GLY A -11 REMARK 465 ALA A -10 REMARK 465 SER A -9 REMARK 465 THR A -8 REMARK 465 SER A -7 REMARK 465 LEU A -6 REMARK 465 TYR A -5 REMARK 465 LYS A -4 REMARK 465 LYS A -3 REMARK 465 ALA A -2 REMARK 465 GLY A -1 REMARK 465 LEU A 0 REMARK 465 MET A 1 REMARK 465 GLU A 510 REMARK 465 GLU A 511 REMARK 465 SER A 512 REMARK 465 SER A 513 REMARK 465 PHE A 514 REMARK 465 GLU A 515 REMARK 465 GLU A 516 REMARK 465 LYS A 517 REMARK 465 SER A 518 REMARK 465 GLU A 519 REMARK 465 THR A 520 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 DA C 1 O5' 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 DC C 11 O3' DC C 11 C3' -0.039 REMARK 500 DT D 5 O3' DT D 5 C3' -0.037 REMARK 500 DC D 10 O3' DC D 10 C3' -0.041 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 DA C 1 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC C 2 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DC C 2 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 7 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DG C 13 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DT C 15 O4' - C1' - C2' ANGL. DEV. = 3.0 DEGREES REMARK 500 DT D 1 N3 - C4 - O4 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT D 1 C5 - C4 - O4 ANGL. DEV. = -4.7 DEGREES REMARK 500 DG D 8 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA D 9 O4' - C1' - N9 ANGL. DEV. = 3.8 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 13 -58.47 -124.23 REMARK 500 LYS A 14 -167.99 -116.33 REMARK 500 ALA A 34 76.20 -119.99 REMARK 500 SER A 80 -151.15 -122.19 REMARK 500 ASN A 151 32.65 -96.86 REMARK 500 THR A 258 -164.52 -114.89 REMARK 500 THR A 376 -108.33 -97.96 REMARK 500 ASP A 379 -66.48 -134.01 REMARK 500 GLN A 398 117.07 -39.32 REMARK 500 PHE A 415 -40.60 73.96 REMARK 500 CYS A 453 11.50 -145.60 REMARK 500 THR A 474 -62.27 -120.09 REMARK 500 REMARK 500 REMARK: NULL 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 1510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WB2 RELATED DB: PDB REMARK 900 DROSOPHILA MELANOGASTER (6-4) PHOTOLYASE BOUND TO DOUBLE STRANDED REMARK 900 DNA CONTAINING A T(6 -4)C PHOTOLESION REMARK 900 RELATED ID: 2WQ7 RELATED DB: PDB REMARK 900 STRUCTURE OF THE 6-4 PHOTOLYASE OF D. MELANOGASTER IN COMPLEX WITH REMARK 900 THE NON-NATURAL N4-METHYL T(6-4)C LESION DBREF 2WQ6 A -22 0 PDB 2WQ6 2WQ6 -22 0 DBREF 2WQ6 A 1 520 UNP Q8SXK5 Q8SXK5_DROME 1 520 DBREF 2WQ6 C 1 15 PDB 2WQ6 2WQ6 1 15 DBREF 2WQ6 D 1 15 PDB 2WQ6 2WQ6 1 15 SEQRES 1 A 543 MET ALA SER TRP SER HIS PRO GLN PHE GLU LYS GLY ALA SEQRES 2 A 543 SER THR SER LEU TYR LYS LYS ALA GLY LEU MET ASP SER SEQRES 3 A 543 GLN ARG SER THR LEU VAL HIS TRP PHE ARG LYS GLY LEU SEQRES 4 A 543 ARG LEU HIS ASP ASN PRO ALA LEU SER HIS ILE PHE THR SEQRES 5 A 543 ALA ALA ASN ALA ALA PRO GLY ARG TYR PHE VAL ARG PRO SEQRES 6 A 543 ILE PHE ILE LEU ASP PRO GLY ILE LEU ASP TRP MET GLN SEQRES 7 A 543 VAL GLY ALA ASN ARG TRP ARG PHE LEU GLN GLN THR LEU SEQRES 8 A 543 GLU ASP LEU ASP ASN GLN LEU ARG LYS LEU ASN SER ARG SEQRES 9 A 543 LEU PHE VAL VAL ARG GLY LYS PRO ALA GLU VAL PHE PRO SEQRES 10 A 543 ARG ILE PHE LYS SER TRP ARG VAL GLU MET LEU THR PHE SEQRES 11 A 543 GLU THR ASP ILE GLU PRO TYR SER VAL THR ARG ASP ALA SEQRES 12 A 543 ALA VAL GLN LYS LEU ALA LYS ALA GLU GLY VAL ARG VAL SEQRES 13 A 543 GLU THR HIS CYS SER HIS THR ILE TYR ASN PRO GLU LEU SEQRES 14 A 543 VAL ILE ALA LYS ASN LEU GLY LYS ALA PRO ILE THR TYR SEQRES 15 A 543 GLN LYS PHE LEU GLY ILE VAL GLU GLN LEU LYS VAL PRO SEQRES 16 A 543 LYS VAL LEU GLY VAL PRO GLU LYS LEU LYS ASN MET PRO SEQRES 17 A 543 THR PRO PRO LYS ASP GLU VAL GLU GLN LYS ASP SER ALA SEQRES 18 A 543 ALA TYR ASP CYS PRO THR MET LYS GLN LEU VAL LYS ARG SEQRES 19 A 543 PRO GLU GLU LEU GLY PRO ASN LYS PHE PRO GLY GLY GLU SEQRES 20 A 543 THR GLU ALA LEU ARG ARG MET GLU GLU SER LEU LYS ASP SEQRES 21 A 543 GLU ILE TRP VAL ALA ARG PHE GLU LYS PRO ASN THR ALA SEQRES 22 A 543 PRO ASN SER LEU GLU PRO SER THR THR VAL LEU SER PRO SEQRES 23 A 543 TYR LEU LYS PHE GLY CYS LEU SER ALA ARG LEU PHE ASN SEQRES 24 A 543 GLN LYS LEU LYS GLU ILE ILE LYS ARG GLN PRO LYS HIS SEQRES 25 A 543 SER GLN PRO PRO VAL SER LEU ILE GLY GLN LEU MET TRP SEQRES 26 A 543 ARG GLU PHE TYR TYR THR VAL ALA ALA ALA GLU PRO ASN SEQRES 27 A 543 PHE ASP ARG MET LEU GLY ASN VAL TYR CYS MET GLN ILE SEQRES 28 A 543 PRO TRP GLN GLU HIS PRO ASP HIS LEU GLU ALA TRP THR SEQRES 29 A 543 HIS GLY ARG THR GLY TYR PRO PHE ILE ASP ALA ILE MET SEQRES 30 A 543 ARG GLN LEU ARG GLN GLU GLY TRP ILE HIS HIS LEU ALA SEQRES 31 A 543 ARG HIS ALA VAL ALA CYS PHE LEU THR ARG GLY ASP LEU SEQRES 32 A 543 TRP ILE SER TRP GLU GLU GLY GLN ARG VAL PHE GLU GLN SEQRES 33 A 543 LEU LEU LEU ASP GLN ASP TRP ALA LEU ASN ALA GLY ASN SEQRES 34 A 543 TRP MET TRP LEU SER ALA SER ALA PHE PHE HIS GLN TYR SEQRES 35 A 543 PHE ARG VAL TYR SER PRO VAL ALA PHE GLY LYS LYS THR SEQRES 36 A 543 ASP PRO GLN GLY HIS TYR ILE ARG LYS TYR VAL PRO GLU SEQRES 37 A 543 LEU SER LYS TYR PRO ALA GLY CYS ILE TYR GLU PRO TRP SEQRES 38 A 543 LYS ALA SER LEU VAL ASP GLN ARG ALA TYR GLY CYS VAL SEQRES 39 A 543 LEU GLY THR ASP TYR PRO HIS ARG ILE VAL LYS HIS GLU SEQRES 40 A 543 VAL VAL HIS LYS GLU ASN ILE LYS ARG MET GLY ALA ALA SEQRES 41 A 543 TYR LYS VAL ASN ARG GLU VAL ARG THR GLY LYS GLU GLU SEQRES 42 A 543 GLU SER SER PHE GLU GLU LYS SER GLU THR SEQRES 1 C 15 DA DC DA DG DC DG DG TDY CDW DG DC DA DG SEQRES 2 C 15 DG DT SEQRES 1 D 15 DT DA DC DC DT DG DC DG DA DC DC DG DC SEQRES 2 D 15 DT DG MODRES 2WQ6 TDY C 8 DT MODRES 2WQ6 CDW C 9 DC HET TDY C 8 22 HET CDW C 9 18 HET FAD A1510 53 HETNAM TDY 5-(METHYLAMINO)THYMIDINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM CDW (4R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 CDW PENTOFURANOSYL)-1,3-DIAZABICYCLO[2.2.0]HEX-5-EN-2-ONE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 TDY C11 H20 N3 O8 P FORMUL 2 CDW C9 H13 N2 O7 P FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 HOH *170(H2 O) HELIX 1 1 ASN A 21 ALA A 34 1 14 HELIX 2 2 ALA A 58 LEU A 78 1 21 HELIX 3 3 LYS A 88 TRP A 100 1 13 HELIX 4 4 GLU A 112 GLU A 129 1 18 HELIX 5 5 ASN A 143 ASN A 151 1 9 HELIX 6 6 THR A 158 LEU A 163 1 6 HELIX 7 7 ILE A 165 LEU A 169 5 5 HELIX 8 8 ASP A 190 ASP A 196 1 7 HELIX 9 9 THR A 204 VAL A 209 1 6 HELIX 10 10 ARG A 211 LEU A 215 5 5 HELIX 11 11 GLU A 224 LEU A 235 1 12 HELIX 12 12 ASP A 237 ARG A 243 1 7 HELIX 13 13 GLU A 245 THR A 249 5 5 HELIX 14 14 LEU A 261 PHE A 267 1 7 HELIX 15 15 SER A 271 GLN A 286 1 16 HELIX 16 16 GLN A 299 ALA A 312 1 14 HELIX 17 17 HIS A 333 HIS A 342 1 10 HELIX 18 18 TYR A 347 GLU A 360 1 14 HELIX 19 19 HIS A 364 THR A 376 1 13 HELIX 20 20 GLN A 388 LEU A 395 1 8 HELIX 21 21 ASP A 399 ALA A 404 1 6 HELIX 22 22 ASN A 406 SER A 411 1 6 HELIX 23 23 HIS A 437 VAL A 443 1 7 HELIX 24 24 PRO A 444 SER A 447 5 4 HELIX 25 25 GLU A 456 ALA A 460 5 5 HELIX 26 26 SER A 461 TYR A 468 1 8 HELIX 27 27 LYS A 482 MET A 494 1 13 HELIX 28 28 ALA A 496 THR A 506 1 11 SHEET 1 AA 5 PHE A 83 VAL A 85 0 SHEET 2 AA 5 TYR A 38 ILE A 45 1 O PRO A 42 N PHE A 83 SHEET 3 AA 5 SER A 6 PHE A 12 1 O SER A 6 N PHE A 39 SHEET 4 AA 5 VAL A 102 GLU A 108 1 N GLU A 103 O THR A 7 SHEET 5 AA 5 ARG A 132 HIS A 136 1 O ARG A 132 N LEU A 105 LINK O3' DG C 7 P TDY C 8 1555 1555 1.56 LINK C6 TDY C 8 C4 CDW C 9 1555 1555 1.52 LINK O3' TDY C 8 P CDW C 9 1555 1555 1.57 LINK O3' CDW C 9 P DG C 10 1555 1555 1.57 CISPEP 1 PRO A 292 PRO A 293 0 0.58 SITE 1 AC1 26 PHE A 244 LYS A 246 THR A 258 THR A 259 SITE 2 AC1 26 VAL A 260 LEU A 261 SER A 262 LEU A 265 SITE 3 AC1 26 GLN A 299 ARG A 303 TYR A 306 TRP A 362 SITE 4 AC1 26 HIS A 365 ARG A 368 HIS A 369 LEU A 395 SITE 5 AC1 26 ASP A 397 GLN A 398 ASP A 399 LEU A 402 SITE 6 AC1 26 ASN A 403 ASN A 406 LEU A 410 HOH A2153 SITE 7 AC1 26 HOH A2154 TDY C 8 CRYST1 89.169 87.486 91.856 90.00 90.00 90.00 P 21 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 0.011215 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011430 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010887 0.00000