HEADER LYASE 24-SEP-10 2XRY TITLE X-RAY STRUCTURE OF ARCHAEAL CLASS II CPD PHOTOLYASE FROM TITLE 2 METHANOSARCINA MAZEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYRIBODIPYRIMIDINE PHOTOLYASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 3-464; COMPND 5 SYNONYM: CLASS II CPD PHOTOLYASE; COMPND 6 EC: 4.1.99.3; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA MAZEI; SOURCE 3 ORGANISM_TAXID: 192952; SOURCE 4 STRAIN: GO1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS DNA DAMAGE, DNA REPAIR, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.KIONTKE,Y.GEISSELBRECHT,R.POKORNY,T.CARELL,A.BATSCHAUER,L.O.ESSEN REVDAT 3 01-MAY-24 2XRY 1 REMARK REVDAT 2 16-NOV-11 2XRY 1 JRNL REVDAT 1 14-SEP-11 2XRY 0 JRNL AUTH S.KIONTKE,Y.GEISSELBRECHT,R.POKORNY,T.CARELL,A.BATSCHAUER, JRNL AUTH 2 L.O.ESSEN JRNL TITL CRYSTAL STRUCTURES OF AN ARCHAEAL CLASS II DNA PHOTOLYASE JRNL TITL 2 AND ITS COMPLEX WITH UV-DAMAGED DUPLEX DNA. JRNL REF EMBO J. V. 30 4437 2011 JRNL REFN ISSN 0261-4189 JRNL PMID 21892138 JRNL DOI 10.1038/EMBOJ.2011.313 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 94089 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1416 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6759 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3677 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 110 REMARK 3 SOLVENT ATOMS : 375 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.32000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -0.64000 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): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.055 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4016 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2765 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5487 ; 1.378 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6748 ; 0.867 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 503 ; 5.072 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;31.110 ;23.825 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 681 ;12.782 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;19.335 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 570 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4414 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 831 ; 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): 2358 ; 2.161 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 941 ; 0.748 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3826 ; 3.221 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1658 ; 3.253 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1637 ; 4.802 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -4 A 212 REMARK 3 ORIGIN FOR THE GROUP (A): 4.6984 23.6185 107.6981 REMARK 3 T TENSOR REMARK 3 T11: 0.0049 T22: 0.1034 REMARK 3 T33: 0.0589 T12: 0.0019 REMARK 3 T13: -0.0081 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 0.7023 L22: 0.6174 REMARK 3 L33: 1.1030 L12: 0.0133 REMARK 3 L13: 0.0193 L23: 0.0976 REMARK 3 S TENSOR REMARK 3 S11: -0.0280 S12: 0.0350 S13: -0.0287 REMARK 3 S21: -0.0139 S22: -0.0096 S23: 0.1522 REMARK 3 S31: 0.0181 S32: -0.2380 S33: 0.0376 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 213 A 462 REMARK 3 RESIDUE RANGE : A 1463 A 1463 REMARK 3 ORIGIN FOR THE GROUP (A): 30.1214 25.7004 102.1939 REMARK 3 T TENSOR REMARK 3 T11: 0.0094 T22: 0.0701 REMARK 3 T33: 0.0358 T12: 0.0020 REMARK 3 T13: 0.0040 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.7165 L22: 0.3863 REMARK 3 L33: 1.1647 L12: -0.1113 REMARK 3 L13: 0.2795 L23: -0.1146 REMARK 3 S TENSOR REMARK 3 S11: -0.0219 S12: 0.1306 S13: 0.0121 REMARK 3 S21: -0.0437 S22: -0.0267 S23: -0.0730 REMARK 3 S31: -0.0189 S32: 0.1784 S33: 0.0487 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 189-197 ARE REMARK 3 DISORDERED. REMARK 4 REMARK 4 2XRY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1290042654. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-08 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 : 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) : 0.88567 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: UNPUBLISHED STRUCTURAL DATA OF M. BARKERI REMARK 200 PHOTOLYASE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M LITHIUM SULFATE, 7.5% (W/V) PEG REMARK 280 8000 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 121.54000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.88500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 182.31000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.88500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.88500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.77000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.88500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.88500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 182.31000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.88500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.88500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.77000 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 121.54000 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, MET 377 TO THR 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 -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 SER A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 SER A -7 REMARK 465 SER A -6 REMARK 465 GLY A -5 REMARK 465 GLU A 189 REMARK 465 LEU A 190 REMARK 465 SER A 191 REMARK 465 ALA A 192 REMARK 465 GLY A 193 REMARK 465 ALA A 194 REMARK 465 GLY A 195 REMARK 465 MET A 196 REMARK 465 VAL A 197 REMARK 465 ALA A 463 REMARK 465 LEU A 464 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 LEU A -4 CG CD1 CD2 REMARK 470 ARG A -1 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 94 NE CZ NH1 NH2 REMARK 470 LYS A 106 CD CE NZ REMARK 470 LEU A 218 CG CD1 CD2 REMARK 470 LYS A 219 CG CD CE NZ REMARK 470 ASN A 220 CG OD1 ND2 REMARK 470 LYS A 221 CG CD CE NZ REMARK 470 LYS A 238 CD CE NZ REMARK 470 GLU A 348 CD OE1 OE2 REMARK 470 LYS A 394 CE NZ REMARK 470 LYS A 455 CD CE NZ 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 O1 SO4 A 1470 O HOH A 2367 2.11 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 SER A 26 -64.20 -143.39 REMARK 500 ASP A 28 79.30 -113.29 REMARK 500 ALA A 64 -147.54 -117.42 REMARK 500 LEU A 303 -64.32 -95.47 REMARK 500 VAL A 436 -62.13 68.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. 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 1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1466 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1467 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1468 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1469 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1471 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1472 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1473 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1474 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2XRZ RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF ARCHAEAL CLASS II CPD PHOTOLYASE FROM REMARK 900 METHANOSARCINA MAZEI IN COMPLEX WITH INTACT CPD-LESION REMARK 999 REMARK 999 SEQUENCE REMARK 999 2 RESIDUES (MET, ILE) DELETED AT THE 6 N-TERMINUS. DBREF 2XRY A 3 464 UNP Q8PYK9 Q8PYK9_METMA 3 464 SEQADV 2XRY MET A -17 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY GLY A -16 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY SER A -15 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY SER A -14 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY HIS A -13 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY HIS A -12 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY HIS A -11 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY HIS A -10 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY HIS A -9 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY HIS A -8 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY SER A -7 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY SER A -6 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY GLY A -5 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY LEU A -4 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY VAL A -3 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY PRO A -2 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY ARG A -1 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY GLY A 0 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY SER A 1 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY HIS A 2 UNP Q8PYK9 EXPRESSION TAG SEQADV 2XRY THR A 377 UNP Q8PYK9 MET 377 ENGINEERED MUTATION SEQRES 1 A 482 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 482 LEU VAL PRO ARG GLY SER HIS MET ASN PRO LYS ARG ILE SEQRES 3 A 482 ARG ALA LEU LYS SER GLY LYS GLN GLY ASP GLY PRO VAL SEQRES 4 A 482 VAL TYR TRP MET SER ARG ASP GLN ARG ALA GLU ASP ASN SEQRES 5 A 482 TRP ALA LEU LEU PHE SER ARG ALA ILE ALA LYS GLU ALA SEQRES 6 A 482 ASN VAL PRO VAL VAL VAL VAL PHE CYS LEU THR ASP GLU SEQRES 7 A 482 PHE LEU GLU ALA GLY ILE ARG GLN TYR GLU PHE MET LEU SEQRES 8 A 482 LYS GLY LEU GLN GLU LEU GLU VAL SER LEU SER ARG LYS SEQRES 9 A 482 LYS ILE PRO SER PHE PHE LEU ARG GLY ASP PRO GLY GLU SEQRES 10 A 482 LYS ILE SER ARG PHE VAL LYS ASP TYR ASN ALA GLY THR SEQRES 11 A 482 LEU VAL THR ASP PHE SER PRO LEU ARG ILE LYS ASN GLN SEQRES 12 A 482 TRP ILE GLU LYS VAL ILE SER GLY ILE SER ILE PRO PHE SEQRES 13 A 482 PHE GLU VAL ASP ALA HIS ASN VAL VAL PRO CYS TRP GLU SEQRES 14 A 482 ALA SER GLN LYS HIS GLU TYR ALA ALA HIS THR PHE ARG SEQRES 15 A 482 PRO LYS LEU TYR ALA LEU LEU PRO GLU PHE LEU GLU GLU SEQRES 16 A 482 PHE PRO GLU LEU GLU PRO ASN SER VAL THR PRO GLU LEU SEQRES 17 A 482 SER ALA GLY ALA GLY MET VAL GLU THR LEU SER ASP VAL SEQRES 18 A 482 LEU GLU THR GLY VAL LYS ALA LEU LEU PRO GLU ARG ALA SEQRES 19 A 482 LEU LEU LYS ASN LYS ASP PRO LEU PHE GLU PRO TRP HIS SEQRES 20 A 482 PHE GLU PRO GLY GLU LYS ALA ALA LYS LYS VAL MET GLU SEQRES 21 A 482 SER PHE ILE ALA ASP ARG LEU ASP SER TYR GLY ALA LEU SEQRES 22 A 482 ARG ASN ASP PRO THR LYS ASN MET LEU SER ASN LEU SER SEQRES 23 A 482 PRO TYR LEU HIS PHE GLY GLN ILE SER SER GLN ARG VAL SEQRES 24 A 482 VAL LEU GLU VAL GLU LYS ALA GLU SER ASN PRO GLY SER SEQRES 25 A 482 LYS LYS ALA PHE LEU ASP GLU ILE LEU ILE TRP LYS GLU SEQRES 26 A 482 ILE SER ASP ASN PHE CYS TYR TYR ASN PRO GLY TYR ASP SEQRES 27 A 482 GLY PHE GLU SER PHE PRO SER TRP ALA LYS GLU SER LEU SEQRES 28 A 482 ASN ALA HIS ARG ASN ASP VAL ARG SER HIS ILE TYR THR SEQRES 29 A 482 LEU GLU GLU PHE GLU ALA GLY LYS THR HIS ASP PRO LEU SEQRES 30 A 482 TRP ASN ALA SER GLN MET GLU LEU LEU SER THR GLY LYS SEQRES 31 A 482 MET HIS GLY TYR THR ARG MET TYR TRP ALA LYS LYS ILE SEQRES 32 A 482 LEU GLU TRP SER GLU SER PRO GLU LYS ALA LEU GLU ILE SEQRES 33 A 482 ALA ILE CYS LEU ASN ASP ARG TYR GLU LEU ASP GLY ARG SEQRES 34 A 482 ASP PRO ASN GLY TYR ALA GLY ILE ALA TRP SER ILE GLY SEQRES 35 A 482 GLY VAL HIS ASP ARG ALA TRP GLY GLU ARG GLU VAL THR SEQRES 36 A 482 GLY LYS ILE ARG TYR MET SER TYR GLU GLY CYS LYS ARG SEQRES 37 A 482 LYS PHE ASP VAL LYS LEU TYR ILE GLU LYS TYR SER ALA SEQRES 38 A 482 LEU HET FAD A1463 53 HET SO4 A1464 5 HET SO4 A1465 5 HET SO4 A1466 5 HET SO4 A1467 5 HET SO4 A1468 5 HET SO4 A1469 5 HET SO4 A1470 5 HET SO4 A1471 5 HET SO4 A1472 5 HET GOL A1473 6 HET GOL A1474 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 SO4 9(O4 S 2-) FORMUL 12 GOL 2(C3 H8 O3) FORMUL 14 HOH *375(H2 O) HELIX 1 1 PRO A 5 ARG A 7 5 3 HELIX 2 2 TRP A 35 ALA A 47 1 13 HELIX 3 3 PHE A 61 GLU A 63 5 3 HELIX 4 4 ILE A 66 LYS A 86 1 21 HELIX 5 5 PRO A 97 TYR A 108 1 12 HELIX 6 6 ARG A 121 SER A 132 1 12 HELIX 7 7 CYS A 149 ALA A 152 1 4 HELIX 8 8 ALA A 160 PHE A 174 1 15 HELIX 9 9 LEU A 200 LEU A 211 1 12 HELIX 10 10 LEU A 212 GLU A 214 5 3 HELIX 11 11 GLU A 234 ARG A 248 1 15 HELIX 12 12 LEU A 249 SER A 251 5 3 HELIX 13 13 TYR A 252 ARG A 256 1 5 HELIX 14 14 LEU A 267 PHE A 273 1 7 HELIX 15 15 SER A 278 LYS A 287 1 10 HELIX 16 16 SER A 294 TYR A 315 1 22 HELIX 17 17 PHE A 322 SER A 324 5 3 HELIX 18 18 SER A 327 HIS A 336 1 10 HELIX 19 19 LEU A 347 ALA A 352 1 6 HELIX 20 20 PRO A 358 THR A 370 1 13 HELIX 21 21 GLY A 375 TRP A 388 1 14 HELIX 22 22 PRO A 392 TYR A 406 1 15 HELIX 23 23 PRO A 413 GLY A 424 1 12 HELIX 24 24 TYR A 445 LYS A 451 1 7 HELIX 25 25 VAL A 454 TYR A 461 1 8 SHEET 1 AA 6 ILE A 8 LYS A 12 0 SHEET 2 AA 6 PHE A 138 VAL A 141 -1 O PHE A 138 N LEU A 11 SHEET 3 AA 6 THR A 112 THR A 115 1 O LEU A 113 N PHE A 139 SHEET 4 AA 6 VAL A 21 TRP A 24 1 O VAL A 22 N VAL A 114 SHEET 5 AA 6 VAL A 51 LEU A 57 1 O VAL A 52 N TYR A 23 SHEET 6 AA 6 SER A 90 ARG A 94 1 O PHE A 91 N PHE A 55 SITE 1 AC1 31 TYR A 252 LEU A 264 SER A 265 ASN A 266 SITE 2 AC1 31 LEU A 267 SER A 268 LEU A 271 PHE A 298 SITE 3 AC1 31 GLU A 301 ILE A 302 TRP A 305 LYS A 306 SITE 4 AC1 31 SER A 309 LYS A 372 GLY A 375 ARG A 378 SITE 5 AC1 31 MET A 379 ALA A 382 ASN A 403 ASP A 409 SITE 6 AC1 31 GLY A 410 ASN A 414 GLY A 415 SER A 422 SITE 7 AC1 31 GOL A1474 HOH A2084 HOH A2354 HOH A2355 SITE 8 AC1 31 HOH A2356 HOH A2357 HOH A2375 SITE 1 AC2 10 GLY A 65 ILE A 66 ARG A 67 ARG A 215 SITE 2 AC2 10 ALA A 216 PHE A 225 ARG A 405 HOH A2179 SITE 3 AC2 10 HOH A2358 HOH A2359 SITE 1 AC3 5 ALA A 160 HIS A 161 ARG A 164 HOH A2325 SITE 2 AC3 5 HOH A2360 SITE 1 AC4 10 LYS A 129 HIS A 156 TYR A 158 PRO A 326 SITE 2 AC4 10 HOH A2151 HOH A2265 HOH A2361 HOH A2362 SITE 3 AC4 10 HOH A2363 HOH A2366 SITE 1 AC5 6 GLN A 77 GLU A 80 LEU A 200 SER A 201 SITE 2 AC5 6 HOH A2072 HOH A2077 SITE 1 AC6 5 LYS A 449 PHE A 452 ASP A 453 VAL A 454 SITE 2 AC6 5 LYS A 455 SITE 1 AC7 9 LYS A 74 PRO A 292 GLY A 293 SER A 294 SITE 2 AC7 9 LYS A 295 LYS A 296 HOH A2071 HOH A2242 SITE 3 AC7 9 HOH A2365 SITE 1 AC8 9 ASP A 96 GLY A 98 GLU A 99 SER A 327 SITE 2 AC8 9 LYS A 330 HOH A2362 HOH A2366 HOH A2367 SITE 3 AC8 9 HOH A2368 SITE 1 AC9 5 SER A 153 GLN A 154 LYS A 166 HOH A2143 SITE 2 AC9 5 HOH A2369 SITE 1 BC1 7 SER A 26 ARG A 27 SER A 118 HOH A2118 SITE 2 BC1 7 HOH A2231 HOH A2370 HOH A2371 SITE 1 BC2 8 ARG A 121 ILE A 122 TYR A 319 ASP A 320 SITE 2 BC2 8 TYR A 416 HOH A2322 HOH A2372 HOH A2373 SITE 1 BC3 7 TRP A 305 MET A 379 GLY A 418 TRP A 421 SITE 2 BC3 7 FAD A1463 HOH A2374 HOH A2375 CRYST1 69.770 69.770 243.080 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 0.014333 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004114 0.00000