HEADER LYASE 01-NOV-13 4CDM TITLE CRYSTAL STRUCTURE OF M. MAZEI PHOTOLYASE SOAKED WITH SYNTHETIC 8-HDF 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 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 LYASE, DNA REPAIR, ANTENNA CHROMOPHORE EXPDTA X-RAY DIFFRACTION AUTHOR S.KIONTKE,A.BATSCHAUER,L.-O.ESSEN REVDAT 4 08-MAY-24 4CDM 1 REMARK REVDAT 3 13-AUG-14 4CDM 1 JRNL REVDAT 2 04-JUN-14 4CDM 1 JRNL REVDAT 1 21-MAY-14 4CDM 0 JRNL AUTH S.KIONTKE,P.GNAU,R.HASELSBERGER,A.BATSCHAUER,L.ESSEN JRNL TITL STRUCTURAL AND EVOLUTIONARY ASPECTS OF ANTENNA CHROMOPHORE JRNL TITL 2 USAGE BY CLASS II PHOTOLYASES. JRNL REF J.BIOL.CHEM. V. 289 19659 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24849603 JRNL DOI 10.1074/JBC.M113.542431 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.1 REMARK 3 NUMBER OF REFLECTIONS : 15081 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.400 REMARK 3 FREE R VALUE TEST SET COUNT : 216 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 838 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 11 REMARK 3 BIN FREE R VALUE : 0.3560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3639 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 111 REMARK 3 SOLVENT ATOMS : 33 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : -1.17000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.385 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.254 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.291 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.912 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.853 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3897 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5294 ; 1.278 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 460 ; 5.644 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;34.356 ;23.743 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;16.591 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;19.531 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 546 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2965 ; 0.005 ; 0.021 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): 2295 ; 0.514 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3684 ; 1.004 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1602 ; 1.292 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1609 ; 2.254 ; 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 : 1.20 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 REFINED INDIVIDUALLY. RESIDUES 60 TO 64 HAVE REMARK 3 ALTERNATIVE CONFORMATIONS, RESIDUES 190 TO 197 ARE DISORDERED REMARK 4 REMARK 4 4CDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-NOV-13. REMARK 100 THE DEPOSITION ID IS D_1290058825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87260 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15494 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.32000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 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 122.76000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.94500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.94500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 184.14000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.94500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.94500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.38000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.94500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.94500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 184.14000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.94500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.94500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.38000 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 122.76000 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 -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 LEU A -4 REMARK 465 VAL A -3 REMARK 465 PRO A -2 REMARK 465 ARG A -1 REMARK 465 GLY A 0 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 LYS A 15 CG CD CE NZ REMARK 470 GLU A 60 CG CD OE1 OE2 REMARK 470 ARG A 85 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 189 CG CD OE1 OE2 REMARK 470 GLU A 205 CG CD OE1 OE2 REMARK 470 LYS A 209 CG 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 ASP A 222 CG OD1 OD2 REMARK 470 GLU A 390 CG CD OE1 OE2 REMARK 470 GLU A 446 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 26 -68.15 -143.66 REMARK 500 ASP A 59 51.89 -69.92 REMARK 500 ASP A 59 63.19 -69.92 REMARK 500 GLU A 60 145.30 -170.46 REMARK 500 GLU A 60 146.36 88.09 REMARK 500 PHE A 61 -18.89 123.73 REMARK 500 LEU A 62 41.24 27.42 REMARK 500 GLU A 63 -124.85 106.98 REMARK 500 ALA A 64 -153.99 -99.58 REMARK 500 ALA A 64 124.91 70.57 REMARK 500 ARG A 85 2.72 -58.22 REMARK 500 LYS A 219 -47.69 -14.29 REMARK 500 ASN A 220 -4.18 -44.23 REMARK 500 ASN A 262 71.44 -105.39 REMARK 500 LYS A 354 43.96 -104.20 REMARK 500 HIS A 356 10.97 -64.76 REMARK 500 VAL A 436 -49.83 67.23 REMARK 500 ARG A 441 124.94 -39.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 FLAVIN-ADENINE DINUCLEOTIDE (FAD): NON-COVALENTLY BOUND. REMARK 600 8-HYDROXY-10-(D-RIBO-2,3,4, 5-TETRAHYDROXYPENTYL) REMARK 600 -5-DEAZAISOALLOXAZINE (FO1): NON-COVALENTLY BOUND 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 FO1 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 GOL A 1469 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1470 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4CDN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF M. MAZEI PHOTOLYASE WITH ITS IN VIVO REMARK 900 RECONSTITUTED 8-HDF ANTENNA CHROMOPHORE REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE CLONFLICT AT POSITION 377 (SEE BELOW) DBREF 4CDM A 3 464 UNP Q8PYK9 Q8PYK9_METMA 3 464 SEQADV 4CDM MET A -17 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM GLY A -16 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM SER A -15 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM SER A -14 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM HIS A -13 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM HIS A -12 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM HIS A -11 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM HIS A -10 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM HIS A -9 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM HIS A -8 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM SER A -7 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM SER A -6 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM GLY A -5 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM LEU A -4 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM VAL A -3 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM PRO A -2 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM ARG A -1 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM GLY A 0 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM SER A 1 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM HIS A 2 UNP Q8PYK9 EXPRESSION TAG SEQADV 4CDM THR A 377 UNP Q8PYK9 MET 377 CLONING ARTIFACT 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 FO1 A1464 26 HET SO4 A1465 5 HET SO4 A1466 5 HET SO4 A1467 5 HET SO4 A1468 5 HET GOL A1469 6 HET GOL A1470 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM FO1 1-DEOXY-1-(8-HYDROXY-2,4-DIOXO-3,4-DIHYDROPYRIMIDO[4,5- HETNAM 2 FO1 B]QUINOLIN-10(2H)-YL)-D-RIBITOL HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN FO1 7,8-DIDEMETHYL-8-HYDROXY-5-DEAZARIBOFLAVIN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 FO1 C16 H17 N3 O7 FORMUL 4 SO4 4(O4 S 2-) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 10 HOH *33(H2 O) HELIX 1 1 ASN A 4 LYS A 6 5 3 HELIX 2 2 ASN A 34 ALA A 47 1 14 HELIX 3 3 GLY A 65 ARG A 85 1 21 HELIX 4 4 ASP A 96 TYR A 108 1 13 HELIX 5 5 LEU A 120 GLY A 133 1 14 HELIX 6 6 PRO A 148 SER A 153 1 6 HELIX 7 7 ALA A 159 ALA A 169 1 11 HELIX 8 8 LEU A 170 LEU A 175 1 6 HELIX 9 9 THR A 199 LEU A 212 1 14 HELIX 10 10 GLU A 226 PHE A 230 5 5 HELIX 11 11 GLY A 233 ARG A 248 1 16 HELIX 12 12 ARG A 248 ARG A 256 1 9 HELIX 13 13 LEU A 267 PHE A 273 1 7 HELIX 14 14 SER A 277 ALA A 288 1 12 HELIX 15 15 GLY A 293 LEU A 303 1 11 HELIX 16 16 LEU A 303 ASN A 316 1 14 HELIX 17 17 GLY A 321 PHE A 325 5 5 HELIX 18 18 PRO A 326 HIS A 336 1 11 HELIX 19 19 THR A 346 ALA A 352 1 7 HELIX 20 20 ASP A 357 GLY A 371 1 15 HELIX 21 21 HIS A 374 TRP A 388 1 15 HELIX 22 22 SER A 391 GLU A 407 1 17 HELIX 23 23 ASP A 412 GLY A 425 1 14 HELIX 24 24 SER A 444 PHE A 452 1 9 HELIX 25 25 ASP A 453 TYR A 461 1 9 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 LEU A 113 ASP A 116 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 SHEET 1 AB 2 LEU A 217 LEU A 218 0 SHEET 2 AB 2 ASP A 222 PRO A 223 -1 O ASP A 222 N LEU A 218 SITE 1 AC1 25 TYR A 252 LEU A 264 SER A 265 ASN A 266 SITE 2 AC1 25 LEU A 267 SER A 268 LEU A 271 PHE A 298 SITE 3 AC1 25 GLU A 301 ILE A 302 TRP A 305 LYS A 306 SITE 4 AC1 25 LYS A 372 GLY A 375 ARG A 378 MET A 379 SITE 5 AC1 25 ALA A 382 ASN A 403 ASP A 409 GLY A 410 SITE 6 AC1 25 ASN A 414 GLY A 415 SER A 422 GOL A1470 SITE 7 AC1 25 HOH A2024 SITE 1 AC2 15 SER A 26 ARG A 27 PHE A 55 CYS A 56 SITE 2 AC2 15 THR A 58 MET A 72 SER A 118 LYS A 123 SITE 3 AC2 15 TRP A 126 HIS A 272 PHE A 273 ARG A 411 SITE 4 AC2 15 HOH A2002 HOH A2003 HOH A2016 SITE 1 AC3 5 ILE A 66 ARG A 67 ARG A 215 ALA A 216 SITE 2 AC3 5 ARG A 405 SITE 1 AC4 5 LYS A 74 PRO A 292 GLY A 293 LYS A 295 SITE 2 AC4 5 LYS A 296 SITE 1 AC5 5 LYS A 449 PHE A 452 ASP A 453 VAL A 454 SITE 2 AC5 5 LYS A 455 SITE 1 AC6 5 GLN A 77 GLU A 80 THR A 199 LEU A 200 SITE 2 AC6 5 SER A 201 SITE 1 AC7 3 ALA A 160 HIS A 161 ARG A 164 SITE 1 AC8 4 TRP A 305 MET A 379 TRP A 421 FAD A1463 CRYST1 69.890 69.890 245.520 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 0.014308 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004073 0.00000