HEADER LYASE 01-AUG-06 2J08 TITLE THERMUS DNA PHOTOLYASE WITH 8-IOD-RIBOFLAVIN ANTENNA CHROMOPHORE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYRIBODIPYRIMIDINE PHOTO-LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DNA PHOTOLYASE, PHOTOREACTIVATING ENZYME; COMPND 5 EC: 4.1.99.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET36B; SOURCE 10 OTHER_DETAILS: GERMAN COLLECTION OF MICROORGANISMS (DSM) KEYWDS LYASE, FLAVOPROTEIN, DNA REPAIR EXPDTA X-RAY DIFFRACTION AUTHOR T.KLAR,G.KAISER,U.HENNECKE,T.CARELL,A.BATSCHAUER,L.-O.ESSEN REVDAT 5 13-DEC-23 2J08 1 REMARK REVDAT 4 05-JUL-17 2J08 1 REMARK REVDAT 3 13-JUL-11 2J08 1 VERSN REVDAT 2 24-FEB-09 2J08 1 VERSN REVDAT 1 01-MAY-07 2J08 0 JRNL AUTH T.KLAR,G.KAISER,U.HENNECKE,T.CARELL,A.BATSCHAUER,L.-O.ESSEN JRNL TITL NATURAL AND NON-NATURAL ANTENNA CHROMOPHORES IN THE DNA JRNL TITL 2 PHOTOLYASE FROM THERMUS THERMOPHILUS JRNL REF CHEMBIOCHEM V. 7 1798 2006 JRNL REFN ISSN 1439-4227 JRNL PMID 17051659 JRNL DOI 10.1002/CBIC.200600206 REMARK 2 REMARK 2 RESOLUTION. 2.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 14393 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) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 771 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) : 2.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 829 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3372 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 92 REMARK 3 SOLVENT ATOMS : 108 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.13000 REMARK 3 B12 (A**2) : 0.04000 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): 2.594 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.348 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.216 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.803 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3582 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4903 ; 2.281 ; 2.003 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 418 ; 9.060 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;32.321 ;21.287 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 522 ;21.169 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;21.861 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 489 ; 0.191 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2841 ; 0.026 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1604 ; 0.264 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2321 ; 0.334 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 176 ; 0.216 ; 0.200 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): 49 ; 0.279 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.142 ; 0.200 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): 2124 ; 2.621 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3359 ; 3.897 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1769 ; 6.521 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1544 ; 8.629 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 260 REMARK 3 RESIDUE RANGE : A 1422 A 1422 REMARK 3 ORIGIN FOR THE GROUP (A): 37.8230 15.7820 27.7610 REMARK 3 T TENSOR REMARK 3 T11: 0.0297 T22: 0.0089 REMARK 3 T33: 0.0304 T12: -0.0035 REMARK 3 T13: -0.0241 T23: 0.0083 REMARK 3 L TENSOR REMARK 3 L11: 1.3010 L22: 0.5735 REMARK 3 L33: 0.9383 L12: -0.4749 REMARK 3 L13: 0.0924 L23: 0.0681 REMARK 3 S TENSOR REMARK 3 S11: -0.0342 S12: -0.0479 S13: 0.0138 REMARK 3 S21: 0.0621 S22: 0.0778 S23: 0.0469 REMARK 3 S31: 0.0725 S32: -0.1122 S33: -0.0436 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 261 A 420 REMARK 3 RESIDUE RANGE : A 1421 A 1421 REMARK 3 ORIGIN FOR THE GROUP (A): 33.6390 15.7770 56.1460 REMARK 3 T TENSOR REMARK 3 T11: 0.1449 T22: 0.2345 REMARK 3 T33: -0.0886 T12: 0.2151 REMARK 3 T13: 0.0243 T23: 0.0206 REMARK 3 L TENSOR REMARK 3 L11: 1.2434 L22: 2.6971 REMARK 3 L33: 2.7231 L12: -0.1693 REMARK 3 L13: 0.2147 L23: -1.2066 REMARK 3 S TENSOR REMARK 3 S11: -0.3071 S12: -0.5735 S13: 0.0006 REMARK 3 S21: 0.7223 S22: 0.4069 S23: 0.0706 REMARK 3 S31: -0.2011 S32: -0.4264 S33: -0.0999 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. REMARK 4 REMARK 4 2J08 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1290029550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19019 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 24.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1IQR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM TRIS-HCL, PH 8.5, 1.0 M REMARK 280 NH4H2PO4, 11.8 MG/ML PROTEIN. CRYSTAL WAS SOAKED WITH 0.1 MM FMN REMARK 280 FOR 90 MIN PRIOR TO FREEZING., PH 8.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.75400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 93.50800 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 70.13100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 116.88500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 23.37700 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.75400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 93.50800 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 116.88500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 70.13100 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 23.37700 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 23.37700 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 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 ARG A 26 CZ NH1 NH2 REMARK 470 LYS A 89 CD CE NZ REMARK 470 LYS A 158 CD CE NZ REMARK 470 ARG A 269 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 419 CG CD NE CZ NH1 NH2 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 ND1 HIS A 15 OE2 GLU A 179 1.70 REMARK 500 NH1 ARG A 46 O1 PO4 A 1424 2.01 REMARK 500 O HOH A 2014 O HOH A 2040 2.08 REMARK 500 NE ARG A 84 O HOH A 2033 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 72 CG GLU A 72 CD 0.130 REMARK 500 TYR A 103 CD1 TYR A 103 CE1 -0.100 REMARK 500 GLU A 277 CG GLU A 277 CD 0.098 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 LEU A 5 CA - CB - CG ANGL. DEV. = 14.0 DEGREES REMARK 500 LEU A 5 CB - CG - CD1 ANGL. DEV. = -11.5 DEGREES REMARK 500 LEU A 14 CB - CG - CD1 ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 46 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 PRO A 166 C - N - CA ANGL. DEV. = -9.7 DEGREES REMARK 500 LEU A 221 CA - CB - CG ANGL. DEV. = 17.0 DEGREES REMARK 500 LEU A 339 CB - CG - CD2 ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG A 366 NE - CZ - NH2 ANGL. DEV. = -3.1 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 9 -118.98 -109.06 REMARK 500 ASP A 11 61.64 -159.01 REMARK 500 ALA A 272 62.34 -105.47 REMARK 500 ASP A 278 96.01 177.68 REMARK 500 ARG A 366 96.36 -68.64 REMARK 500 ASP A 378 61.32 -156.52 REMARK 500 ALA A 388 65.95 -157.95 REMARK 500 PRO A 389 3.51 -67.63 REMARK 500 TYR A 394 2.07 -67.89 REMARK 500 ASP A 398 64.15 36.54 REMARK 500 LEU A 411 -37.27 -35.44 REMARK 500 ASP A 416 -86.20 -56.08 REMARK 500 LEU A 417 -68.61 -11.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 357 GLY A 358 143.52 REMARK 500 ASP A 378 PRO A 379 -141.75 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 47 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU A 77 -11.82 REMARK 500 ARG A 85 -11.31 REMARK 500 PRO A 99 -10.49 REMARK 500 ASP A 105 -11.01 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 CL A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1423 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A1424 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A1421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IRF A1422 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IQR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DNA PHOTOLYASE FROM THERMUSTHERMOPHILUS REMARK 900 RELATED ID: 1IQU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PHOTOLYASE-THYMINE COMPLEX REMARK 900 RELATED ID: 2CGB RELATED DB: PDB REMARK 900 THERMUS DNA PHOTOLYASE WITH FMN ANTENNA CHROMOPHORE REMARK 900 RELATED ID: 2CGC RELATED DB: PDB REMARK 900 THERMUS DNA PHOTOLYASE WITH 8-HDF ANTENNA CHROMOPHORE REMARK 900 RELATED ID: 2J07 RELATED DB: PDB REMARK 900 THERMUS DNA PHOTOLYASE WITH 8-HDF ANTENNA CHROMOPHORE REMARK 900 RELATED ID: 2J09 RELATED DB: PDB REMARK 900 THERMUS DNA PHOTOLYASE WITH FMN CHROMOPHORE DBREF 2J08 A 1 420 UNP P61497 PHR_THET8 1 420 SEQRES 1 A 420 MET GLY PRO LEU LEU VAL TRP HIS ARG GLY ASP LEU ARG SEQRES 2 A 420 LEU HIS ASP HIS PRO ALA LEU LEU GLU ALA LEU ALA ARG SEQRES 3 A 420 GLY PRO VAL VAL GLY LEU VAL VAL LEU ASP PRO ASN ASN SEQRES 4 A 420 LEU LYS THR THR PRO ARG ARG ARG ALA TRP PHE LEU GLU SEQRES 5 A 420 ASN VAL ARG ALA LEU ARG GLU ALA TYR ARG ALA ARG GLY SEQRES 6 A 420 GLY ALA LEU TRP VAL LEU GLU GLY LEU PRO TRP GLU LYS SEQRES 7 A 420 VAL PRO GLU ALA ALA ARG ARG LEU LYS ALA LYS ALA VAL SEQRES 8 A 420 TYR ALA LEU THR SER HIS THR PRO TYR GLY ARG TYR ARG SEQRES 9 A 420 ASP GLY ARG VAL ARG GLU ALA LEU PRO VAL PRO LEU HIS SEQRES 10 A 420 LEU LEU PRO ALA PRO HIS LEU LEU PRO PRO ASP LEU PRO SEQRES 11 A 420 ARG ALA TYR ARG VAL TYR THR PRO PHE SER ARG LEU TYR SEQRES 12 A 420 ARG GLY ALA ALA PRO PRO LEU PRO PRO PRO GLU ALA LEU SEQRES 13 A 420 PRO LYS GLY PRO GLU GLU GLY GLU ILE PRO ARG GLU ASP SEQRES 14 A 420 PRO GLY LEU PRO LEU PRO GLU PRO GLY GLU GLU ALA ALA SEQRES 15 A 420 LEU ALA GLY LEU ARG ALA PHE LEU GLU ALA LYS LEU PRO SEQRES 16 A 420 ARG TYR ALA GLU GLU ARG ASP ARG LEU ASP GLY GLU GLY SEQRES 17 A 420 GLY SER ARG LEU SER PRO TYR PHE ALA LEU GLY VAL LEU SEQRES 18 A 420 SER PRO ARG LEU ALA ALA TRP GLU ALA GLU ARG ARG GLY SEQRES 19 A 420 GLY GLU GLY ALA ARG LYS TRP VAL ALA GLU LEU LEU TRP SEQRES 20 A 420 ARG ASP PHE SER TYR HIS LEU LEU TYR HIS PHE PRO TRP SEQRES 21 A 420 MET ALA GLU ARG PRO LEU ASP PRO ARG PHE GLN ALA PHE SEQRES 22 A 420 PRO TRP GLN GLU ASP GLU ALA LEU PHE GLN ALA TRP TYR SEQRES 23 A 420 GLU GLY LYS THR GLY VAL PRO LEU VAL ASP ALA ALA MET SEQRES 24 A 420 ARG GLU LEU HIS ALA THR GLY PHE LEU SER ASN ARG ALA SEQRES 25 A 420 ARG MET ASN ALA ALA GLN PHE ALA VAL LYS HIS LEU LEU SEQRES 26 A 420 LEU PRO TRP LYS ARG CYS GLU GLU ALA PHE ARG HIS LEU SEQRES 27 A 420 LEU LEU ASP GLY ASP ARG ALA VAL ASN LEU GLN GLY TRP SEQRES 28 A 420 GLN TRP ALA GLY GLY LEU GLY VAL ASP ALA ALA PRO TYR SEQRES 29 A 420 PHE ARG VAL PHE ASN PRO VAL LEU GLN GLY GLU ARG HIS SEQRES 30 A 420 ASP PRO GLU GLY ARG TRP LEU LYS ARG TRP ALA PRO GLU SEQRES 31 A 420 TYR PRO SER TYR ALA PRO LYS ASP PRO VAL VAL ASP LEU SEQRES 32 A 420 GLU GLU ALA ARG ARG ARG TYR LEU ARG LEU ALA ARG ASP SEQRES 33 A 420 LEU ALA ARG GLY HET CL A 901 1 HET CL A 902 1 HET FAD A1421 53 HET IRF A1422 27 HET PO4 A1423 5 HET PO4 A1424 5 HETNAM CL CHLORIDE ION HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM IRF 1-DEOXY-1-(8-IODO-7-METHYL-2,4-DIOXO-3,4- HETNAM 2 IRF DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)-D-RIBITOL HETNAM PO4 PHOSPHATE ION HETSYN IRF 8-IODO-10-(D-RIBO-2,3,4,5-TETRAHYDROXYPENTYL) FORMUL 2 CL 2(CL 1-) FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 IRF C16 H17 I N4 O6 FORMUL 6 PO4 2(O4 P 3-) FORMUL 8 HOH *108(H2 O) HELIX 1 1 HIS A 17 ALA A 25 1 9 HELIX 2 2 ASP A 36 LYS A 41 1 6 HELIX 3 3 THR A 43 ARG A 64 1 22 HELIX 4 4 LEU A 74 LYS A 87 1 14 HELIX 5 5 THR A 98 LEU A 112 1 15 HELIX 6 6 VAL A 135 ARG A 141 1 7 HELIX 7 7 GLY A 178 LYS A 193 1 16 HELIX 8 8 ARG A 196 ARG A 201 1 6 HELIX 9 9 LEU A 212 LEU A 218 1 7 HELIX 10 10 SER A 222 GLY A 234 1 13 HELIX 11 11 GLY A 235 PHE A 258 1 24 HELIX 12 12 PRO A 259 GLU A 263 5 5 HELIX 13 13 ASP A 267 GLN A 271 5 5 HELIX 14 14 ASP A 278 GLU A 287 1 10 HELIX 15 15 VAL A 292 GLY A 306 1 15 HELIX 16 16 SER A 309 HIS A 323 1 15 HELIX 17 17 PRO A 327 LEU A 339 1 13 HELIX 18 18 ASP A 343 GLY A 355 1 13 HELIX 19 19 GLY A 358 ALA A 362 5 5 HELIX 20 20 ASN A 369 ASP A 378 1 10 HELIX 21 21 GLY A 381 ALA A 388 1 8 HELIX 22 22 ASP A 402 GLY A 420 1 19 SHEET 1 AA 5 LEU A 68 GLU A 72 0 SHEET 2 AA 5 VAL A 29 LEU A 35 1 O GLY A 31 N TRP A 69 SHEET 3 AA 5 LEU A 4 TRP A 7 1 O LEU A 4 N VAL A 30 SHEET 4 AA 5 ALA A 90 LEU A 94 1 O ALA A 90 N LEU A 5 SHEET 5 AA 5 LEU A 116 LEU A 119 1 O HIS A 117 N ALA A 93 SITE 1 AC1 2 HIS A 117 HOH A2045 SITE 1 AC2 2 PRO A 148 HOH A2009 SITE 1 AC3 7 VAL A 135 TYR A 136 THR A 137 ARG A 167 SITE 2 AC3 7 ASP A 360 HOH A2107 HOH A2108 SITE 1 AC4 5 THR A 42 ARG A 46 GLU A 77 ARG A 336 SITE 2 AC4 5 HIS A 337 SITE 1 AC5 28 TYR A 197 SER A 210 ARG A 211 LEU A 212 SITE 2 AC5 28 SER A 213 PHE A 216 TRP A 241 GLU A 244 SITE 3 AC5 28 LEU A 245 TRP A 247 ARG A 248 PHE A 307 SITE 4 AC5 28 ASN A 310 ARG A 313 ALA A 317 LEU A 339 SITE 5 AC5 28 ASP A 341 GLY A 342 ASP A 343 VAL A 346 SITE 6 AC5 28 ASN A 347 GLN A 349 GLY A 350 HOH A2089 SITE 7 AC5 28 HOH A2096 HOH A2101 HOH A2102 HOH A2103 SITE 1 AC6 15 ARG A 9 GLY A 10 VAL A 34 LEU A 35 SITE 2 AC6 15 ASP A 36 ASN A 39 LEU A 40 PHE A 50 SITE 3 AC6 15 SER A 96 ARG A 104 LEU A 218 GLY A 342 SITE 4 AC6 15 HOH A2104 HOH A2105 HOH A2106 CRYST1 112.620 112.620 140.262 90.00 90.00 120.00 P 61 2 2 12 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 0.008879 0.005127 0.000000 0.00000 SCALE2 0.000000 0.010253 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007130 0.00000