HEADER DNA BINDING PROTEIN 23-DEC-04 1YD1 TITLE CRYSTAL STRUCTURE OF THE GIY-YIG N-TERMINAL ENDONUCLEASE DOMAIN OF TITLE 2 UVRC FROM THERMOTOGA MARITIMA BOUND TO ITS CATALYTIC DIVALENT CATION: TITLE 3 MAGNESIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: UVRABC SYSTEM PROTEIN C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 SYNONYM: UVRC PROTEIN, EXCINUCLEASE ABC SUBUNIT C; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.TRUGLIO,B.RHAU,D.L.CROTEAU,L.WANG,M.SKORVAGA,E.KARAKAS, AUTHOR 2 M.J.DELLAVECCHIA,H.WANG,B.VAN HOUTEN,C.KISKER REVDAT 5 13-MAR-24 1YD1 1 REMARK LINK REVDAT 4 13-JUL-11 1YD1 1 VERSN REVDAT 3 24-FEB-09 1YD1 1 VERSN REVDAT 2 29-MAR-05 1YD1 1 JRNL REVDAT 1 01-MAR-05 1YD1 0 JRNL AUTH J.J.TRUGLIO,B.RHAU,D.L.CROTEAU,L.WANG,M.SKORVAGA,E.KARAKAS, JRNL AUTH 2 M.J.DELLAVECCHIA,H.WANG,B.VAN HOUTEN,C.KISKER JRNL TITL STRUCTURAL INSIGHTS INTO THE FIRST INCISION REACTION DURING JRNL TITL 2 NUCLEOTIDE EXCISION REPAIR JRNL REF EMBO J. V. 24 885 2005 JRNL REFN ISSN 0261-4189 JRNL PMID 15692561 JRNL DOI 10.1038/SJ.EMBOJ.7600568 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15386 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 830 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1101 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.2310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 738 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 96 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : -0.51000 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): 0.085 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.988 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 755 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 737 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1009 ; 1.473 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1722 ; 0.821 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 88 ; 5.154 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 34 ;30.169 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 158 ;14.126 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;16.922 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 110 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 793 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 146 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 142 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 717 ; 0.173 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 370 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 477 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 54 ; 0.112 ; 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): 5 ; 0.113 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 42 ; 0.306 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.128 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 1.112 ; 0.200 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): 593 ; 1.585 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 179 ; 0.292 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 724 ; 1.641 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 359 ; 3.487 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 285 ; 5.135 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 89 REMARK 3 ORIGIN FOR THE GROUP (A): 42.4754 23.9962 42.9952 REMARK 3 T TENSOR REMARK 3 T11: -0.0050 T22: -0.0457 REMARK 3 T33: -0.0223 T12: -0.0189 REMARK 3 T13: 0.0069 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.2278 L22: 1.7905 REMARK 3 L33: 1.1626 L12: -0.5060 REMARK 3 L13: -0.1310 L23: 1.1424 REMARK 3 S TENSOR REMARK 3 S11: 0.0237 S12: 0.0303 S13: -0.0164 REMARK 3 S21: 0.1038 S22: -0.0577 S23: 0.0020 REMARK 3 S31: 0.0438 S32: -0.0138 S33: 0.0340 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 1YD1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031391. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-04; NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL; NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS; NSLS REMARK 200 BEAMLINE : X26C; X12B; X25 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.1; 1.1; 1.1 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16305 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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; NULL; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, TRIS, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 54.31500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.62300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.62300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 81.47250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.62300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.62300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.15750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.62300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.62300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 81.47250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.62300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.62300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.15750 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 54.31500 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 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 ARG A 90 REMARK 465 LEU A 91 REMARK 465 LYS A 92 REMARK 465 ASP A 93 REMARK 465 THR A 94 REMARK 465 ASP A 95 REMARK 465 PHE A 96 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 MG MG A 2002 O HOH A 2003 3644 0.88 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 LYS A 86 CB LYS A 86 CG -0.211 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 84 63.25 39.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A2001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 76 OE2 REMARK 620 2 HOH A2008 O 91.2 REMARK 620 3 HOH A2013 O 87.5 93.6 REMARK 620 4 HOH A2017 O 87.8 91.7 173.0 REMARK 620 5 HOH A2026 O 179.1 89.5 91.9 92.7 REMARK 620 6 HOH A2030 O 93.0 174.7 89.8 85.2 86.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LN0 RELATED DB: PDB REMARK 900 ENDONUCLEASE DOMAIN OF I-TEVI REMARK 900 RELATED ID: 1MK0 RELATED DB: PDB REMARK 900 ENDONUCLEASE DOMAIN OF I-TEVI REMARK 900 RELATED ID: 1KFT RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE C-TERMINAL DOMAIN OF UVRC FROM E- COLI REMARK 900 RELATED ID: 1D9X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UVRB REMARK 900 RELATED ID: 1YCZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM THERMOTOGA MARITIMA REMARK 900 RELATED ID: 1YD0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM THERMOTOGA MARITIMA BOUND TO MANGANESE REMARK 900 RELATED ID: 1YD2 RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM THERMOTOGA MARITIMA Y19F MUTANT BOUND TO REMARK 900 MANGANESE REMARK 900 RELATED ID: 1YD3 RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM THERMOTOGA MARITIMA Y43F MUTANT BOUND TO REMARK 900 MANGANESE REMARK 900 RELATED ID: 1YD4 RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM THERMOTOGA MARITIMA Y29F MUTANT BOUND TO REMARK 900 MANGANESE REMARK 900 RELATED ID: 1YD5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM THERMOTOGA MARITIMA N88A MUTANT BOUND TO REMARK 900 MANGANESE REMARK 900 RELATED ID: 1YD6 RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM BACILLUS CALDOTENAX DBREF 1YD1 A 1 96 UNP Q9WYA3 UVRC_THEMA 1 96 SEQRES 1 A 96 MET LYS GLU LYS ILE ARG LYS LYS ILE LEU LEU ALA PRO SEQRES 2 A 96 GLU GLU PRO GLY VAL TYR ILE PHE LYS ASN LYS GLY VAL SEQRES 3 A 96 PRO ILE TYR ILE GLY LYS ALA LYS ARG LEU SER ASN ARG SEQRES 4 A 96 LEU ARG SER TYR LEU ASN PRO GLN THR GLU LYS VAL PHE SEQRES 5 A 96 ARG ILE GLY GLU GLU ALA ASP GLU LEU GLU THR ILE VAL SEQRES 6 A 96 VAL MET ASN GLU ARG GLU ALA PHE ILE LEU GLU ALA ASN SEQRES 7 A 96 LEU ILE LYS LYS TYR ARG PRO LYS TYR ASN VAL ARG LEU SEQRES 8 A 96 LYS ASP THR ASP PHE HET MG A2001 1 HET MG A2002 1 HET GOL A1001 6 HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MG 2(MG 2+) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *96(H2 O) HELIX 1 1 LYS A 2 ALA A 12 1 11 HELIX 2 2 ARG A 35 SER A 42 1 8 HELIX 3 3 TYR A 43 ASN A 45 5 3 HELIX 4 4 THR A 48 ALA A 58 1 11 HELIX 5 5 ASN A 68 ARG A 84 1 17 SHEET 1 A 3 VAL A 26 ALA A 33 0 SHEET 2 A 3 GLY A 17 ASN A 23 -1 N PHE A 21 O ILE A 28 SHEET 3 A 3 GLU A 60 VAL A 65 -1 O GLU A 62 N ILE A 20 LINK NH2 ARG A 6 MG MG A2002 3644 1555 2.88 LINK OE2 GLU A 76 MG MG A2001 1555 1555 2.02 LINK MG MG A2001 O HOH A2008 1555 1555 2.13 LINK MG MG A2001 O HOH A2013 1555 1555 2.02 LINK MG MG A2001 O HOH A2017 1555 1555 2.15 LINK MG MG A2001 O HOH A2026 1555 1555 2.13 LINK MG MG A2001 O HOH A2030 1555 1555 2.17 SITE 1 AC1 6 GLU A 76 HOH A2008 HOH A2013 HOH A2017 SITE 2 AC1 6 HOH A2026 HOH A2030 SITE 1 AC2 4 ARG A 6 ASN A 68 ARG A 70 HOH A2003 SITE 1 AC3 7 ILE A 20 LYS A 22 PRO A 27 GLU A 62 SITE 2 AC3 7 TYR A 83 HOH A2056 HOH A2087 CRYST1 55.246 55.246 108.630 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 0.018101 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009206 0.00000