HEADER TRANSFERASE/DNA 22-DEC-03 1RYR TITLE REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*TP*TP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA POLYMERASE IV; COMPND 11 CHAIN: A; COMPND 12 SYNONYM: POL IV; COMPND 13 EC: 2.7.7.7; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 7 ORGANISM_TAXID: 2287; SOURCE 8 GENE: DPO4; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS POLYMERASE, LESION BYPASS, TT-DIMER, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.LING,F.BOUDSOCQ,B.PLOSKY,R.WOODGATE,W.YANG REVDAT 3 04-APR-18 1RYR 1 REMARK REVDAT 2 24-FEB-09 1RYR 1 VERSN REVDAT 1 10-FEB-04 1RYR 0 SPRSDE 10-FEB-04 1RYR 1PM0 JRNL AUTH H.LING,F.BOUDSOCQ,B.PLOSKY,R.WOODGATE,W.YANG JRNL TITL REPLICATION OF A CIS-SYN THYMINE DIMER AT ATOMIC RESOLUTION JRNL REF NATURE V. 424 1083 2003 JRNL REFN ISSN 0028-0836 JRNL PMID 12904819 JRNL DOI 10.1038/NATURE01919 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.34 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 24302 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 SET) : 0.253 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.700 REMARK 3 FREE R VALUE TEST SET COUNT : 648 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.42 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3863 REMARK 3 BIN R VALUE (WORKING SET) : 0.3980 REMARK 3 BIN FREE R VALUE : 0.4480 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 2.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 92 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.047 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2743 REMARK 3 NUCLEIC ACID ATOMS : 587 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.13000 REMARK 3 B22 (A**2) : -1.65000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.39 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.700 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 3.030 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.400 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.650 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.720 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 53.64 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA_HONG_NOV_02.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : ATP.PARAM_Y_REDUCED REMARK 3 PARAMETER FILE 5 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA_HONG.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : ATP.TOP_Y REMARK 3 TOPOLOGY FILE 5 : WATER.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RYR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021158. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.00 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24302 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 19.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : 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: 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 (%): 55.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, CA(AC)2 , PH 7.00, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 49.25950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.77800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.25950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.77800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 GLU A 342 REMARK 465 ALA A 343 REMARK 465 ILE A 344 REMARK 465 GLY A 345 REMARK 465 LEU A 346 REMARK 465 ASP A 347 REMARK 465 LYS A 348 REMARK 465 PHE A 349 REMARK 465 PHE A 350 REMARK 465 ASP A 351 REMARK 465 THR A 352 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 C5 DT C 1904 C5 DT C 1905 1.55 REMARK 500 C6 DT C 1904 C6 DT C 1905 1.57 REMARK 500 O GLU A 235 O HOH A 1819 1.95 REMARK 500 OP1 DT C 1905 O HOH C 25 2.13 REMARK 500 OP1 DT C 1905 O HOH C 59 2.14 REMARK 500 O HOH B 150 O HOH B 159 2.17 REMARK 500 O2G ATP A 1814 O HOH A 1959 2.18 REMARK 500 O HOH A 1940 O HOH A 1968 2.19 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 DT C1903 O3' DT C1903 C3' -0.044 REMARK 500 DT C1904 C4 DT C1904 C5 0.118 REMARK 500 DT C1904 C5 DT C1904 C6 0.217 REMARK 500 DT C1904 C6 DT C1904 N1 0.194 REMARK 500 DT C1905 C4 DT C1905 C5 0.070 REMARK 500 DT C1905 C5 DT C1905 C6 0.221 REMARK 500 DT C1905 C6 DT C1905 N1 0.173 REMARK 500 DT C1905 C5 DT C1905 C7 0.066 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 DC B1813 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT C1903 C2' - C3' - O3' ANGL. DEV. = -18.1 DEGREES REMARK 500 DT C1904 O5' - P - OP1 ANGL. DEV. = 8.0 DEGREES REMARK 500 DT C1904 C6 - N1 - C2 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT C1904 N3 - C4 - C5 ANGL. DEV. = 4.9 DEGREES REMARK 500 DT C1904 C5 - C6 - N1 ANGL. DEV. = -9.4 DEGREES REMARK 500 DT C1904 C5 - C4 - O4 ANGL. DEV. = -7.4 DEGREES REMARK 500 DT C1904 C4 - C5 - C7 ANGL. DEV. = -5.6 DEGREES REMARK 500 DT C1904 C6 - C5 - C7 ANGL. DEV. = -17.7 DEGREES REMARK 500 DT C1904 C6 - N1 - C1' ANGL. DEV. = -9.2 DEGREES REMARK 500 DT C1905 O3' - P - OP2 ANGL. DEV. = -16.7 DEGREES REMARK 500 DT C1905 N1 - C1' - C2' ANGL. DEV. = 9.2 DEGREES REMARK 500 DT C1905 N3 - C4 - C5 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT C1905 C4 - C5 - C6 ANGL. DEV. = -4.0 DEGREES REMARK 500 DT C1905 C5 - C6 - N1 ANGL. DEV. = -7.1 DEGREES REMARK 500 DT C1905 C5 - C4 - O4 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT C1905 C6 - C5 - C7 ANGL. DEV. = -18.3 DEGREES REMARK 500 DT C1912 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 10 55.87 16.48 REMARK 500 ASN A 20 83.02 -157.69 REMARK 500 PHE A 37 -165.84 -173.98 REMARK 500 SER A 96 142.82 177.27 REMARK 500 SER A 103 -177.94 -179.59 REMARK 500 ASP A 113 22.08 -73.10 REMARK 500 SER A 145 -164.48 -169.63 REMARK 500 ASN A 161 44.24 39.92 REMARK 500 MET A 216 -39.76 -177.56 REMARK 500 GLU A 235 107.72 -166.33 REMARK 500 THR A 239 -170.11 -65.29 REMARK 500 SER A 255 152.63 170.43 REMARK 500 ASP A 277 83.59 31.48 REMARK 500 LYS A 278 -17.02 83.22 REMARK 500 ASP A 292 37.95 -94.15 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 DT C1903 0.08 SIDE CHAIN REMARK 500 DT C1904 0.17 SIDE CHAIN REMARK 500 DT C1905 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 ATP A 1814 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 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 105 OD2 REMARK 620 2 HOH A1959 O 79.8 REMARK 620 3 ATP A1814 O2B 103.3 114.1 REMARK 620 4 PHE A 8 O 96.1 77.3 158.8 REMARK 620 5 ASP A 7 OD1 94.7 162.5 83.3 86.9 REMARK 620 6 HOH A1821 O 166.9 99.1 65.0 96.4 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 404 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A1814 O1A REMARK 620 2 ATP A1814 O2B 82.5 REMARK 620 3 ATP A1814 O3A 48.8 53.7 REMARK 620 4 ASP A 105 OD1 155.6 110.9 155.3 REMARK 620 5 HOH A1932 O 82.9 165.3 115.9 82.4 REMARK 620 6 HOH A1963 O 89.4 126.2 137.8 66.2 52.4 REMARK 620 7 HOH A1816 O 83.0 65.8 102.6 84.3 111.1 60.4 REMARK 620 8 ASP A 105 OD2 153.9 71.7 109.3 46.4 122.9 109.1 90.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1814 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RYS RELATED DB: PDB DBREF 1RYR A 1 352 UNP Q97W02 DPO42_SULSO 1 352 DBREF 1RYR B 1801 1813 PDB 1RYR 1RYR 1801 1813 DBREF 1RYR C 1903 1918 PDB 1RYR 1RYR 1903 1918 SEQRES 1 B 13 DG DG DG DG DG DA DA DG DG DA DT DT DC SEQRES 1 C 16 DT DT DT DG DA DA DT DC DC DT DT DC DC SEQRES 2 C 16 DC DC DC SEQRES 1 A 352 MET ILE VAL LEU PHE VAL ASP PHE ASP TYR PHE TYR ALA SEQRES 2 A 352 GLN VAL GLU GLU VAL LEU ASN PRO SER LEU LYS GLY LYS SEQRES 3 A 352 PRO VAL VAL VAL CYS VAL PHE SER GLY ARG PHE GLU ASP SEQRES 4 A 352 SER GLY ALA VAL ALA THR ALA ASN TYR GLU ALA ARG LYS SEQRES 5 A 352 PHE GLY VAL LYS ALA GLY ILE PRO ILE VAL GLU ALA LYS SEQRES 6 A 352 LYS ILE LEU PRO ASN ALA VAL TYR LEU PRO MET ARG LYS SEQRES 7 A 352 GLU VAL TYR GLN GLN VAL SER SER ARG ILE MET ASN LEU SEQRES 8 A 352 LEU ARG GLU TYR SER GLU LYS ILE GLU ILE ALA SER ILE SEQRES 9 A 352 ASP GLU ALA TYR LEU ASP ILE SER ASP LYS VAL ARG ASP SEQRES 10 A 352 TYR ARG GLU ALA TYR ASN LEU GLY LEU GLU ILE LYS ASN SEQRES 11 A 352 LYS ILE LEU GLU LYS GLU LYS ILE THR VAL THR VAL GLY SEQRES 12 A 352 ILE SER LYS ASN LYS VAL PHE ALA LYS ILE ALA ALA ASP SEQRES 13 A 352 MET ALA LYS PRO ASN GLY ILE LYS VAL ILE ASP ASP GLU SEQRES 14 A 352 GLU VAL LYS ARG LEU ILE ARG GLU LEU ASP ILE ALA ASP SEQRES 15 A 352 VAL PRO GLY ILE GLY ASN ILE THR ALA GLU LYS LEU LYS SEQRES 16 A 352 LYS LEU GLY ILE ASN LYS LEU VAL ASP THR LEU SER ILE SEQRES 17 A 352 GLU PHE ASP LYS LEU LYS GLY MET ILE GLY GLU ALA LYS SEQRES 18 A 352 ALA LYS TYR LEU ILE SER LEU ALA ARG ASP GLU TYR ASN SEQRES 19 A 352 GLU PRO ILE ARG THR ARG VAL ARG LYS SER ILE GLY ARG SEQRES 20 A 352 ILE VAL THR MET LYS ARG ASN SER ARG ASN LEU GLU GLU SEQRES 21 A 352 ILE LYS PRO TYR LEU PHE ARG ALA ILE GLU GLU SER TYR SEQRES 22 A 352 TYR LYS LEU ASP LYS ARG ILE PRO LYS ALA ILE HIS VAL SEQRES 23 A 352 VAL ALA VAL THR GLU ASP LEU ASP ILE VAL SER ARG GLY SEQRES 24 A 352 ARG THR PHE PRO HIS GLY ILE SER LYS GLU THR ALA TYR SEQRES 25 A 352 SER GLU SER VAL LYS LEU LEU GLN LYS ILE LEU GLU GLU SEQRES 26 A 352 ASP GLU ARG LYS ILE ARG ARG ILE GLY VAL ARG PHE SER SEQRES 27 A 352 LYS PHE ILE GLU ALA ILE GLY LEU ASP LYS PHE PHE ASP SEQRES 28 A 352 THR HET CA A 402 1 HET CA A 404 1 HET ATP A1814 29 HETNAM CA CALCIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 4 CA 2(CA 2+) FORMUL 6 ATP C10 H16 N5 O13 P3 FORMUL 7 HOH *207(H2 O) HELIX 1 1 TYR A 10 ASN A 20 1 11 HELIX 2 2 PRO A 21 LYS A 24 5 4 HELIX 3 3 ASN A 47 LYS A 52 1 6 HELIX 4 4 PRO A 60 LEU A 68 1 9 HELIX 5 5 ARG A 77 ARG A 93 1 17 HELIX 6 6 SER A 112 VAL A 115 5 4 HELIX 7 7 ASP A 117 LYS A 137 1 21 HELIX 8 8 ASN A 147 LYS A 159 1 13 HELIX 9 9 ASP A 167 LEU A 178 1 12 HELIX 10 10 ASP A 179 VAL A 183 5 5 HELIX 11 11 GLY A 187 LYS A 196 1 10 HELIX 12 12 LYS A 201 SER A 207 5 7 HELIX 13 13 GLU A 209 GLY A 218 1 10 HELIX 14 14 GLY A 218 ARG A 230 1 13 HELIX 15 15 ASN A 257 ASP A 277 1 21 HELIX 16 16 SER A 307 ASP A 326 1 20 SHEET 1 A 5 ILE A 99 SER A 103 0 SHEET 2 A 5 GLU A 106 ASP A 110 -1 O TYR A 108 N GLU A 100 SHEET 3 A 5 VAL A 3 PHE A 8 -1 N LEU A 4 O LEU A 109 SHEET 4 A 5 VAL A 140 SER A 145 -1 O GLY A 143 N PHE A 5 SHEET 5 A 5 ILE A 163 VAL A 165 1 O LYS A 164 N ILE A 144 SHEET 1 B 3 GLY A 41 ALA A 46 0 SHEET 2 B 3 VAL A 28 PHE A 33 -1 N VAL A 30 O THR A 45 SHEET 3 B 3 VAL A 72 PRO A 75 1 O LEU A 74 N CYS A 31 SHEET 1 C 4 SER A 244 SER A 255 0 SHEET 2 C 4 ILE A 330 PHE A 340 -1 O PHE A 337 N ILE A 245 SHEET 3 C 4 PRO A 281 THR A 290 -1 N VAL A 287 O GLY A 334 SHEET 4 C 4 ILE A 295 THR A 301 -1 O VAL A 296 N ALA A 288 LINK CA CA A 402 OD2 ASP A 105 1555 1555 2.25 LINK CA CA A 402 O HOH A1959 1555 1555 1.93 LINK CA CA A 402 O2B ATP A1814 1555 1555 2.40 LINK CA CA A 402 O PHE A 8 1555 1555 2.29 LINK CA CA A 402 OD1 ASP A 7 1555 1555 2.23 LINK CA CA A 402 O HOH A1821 1555 1555 2.62 LINK CA CA A 404 O1A ATP A1814 1555 1555 2.91 LINK CA CA A 404 O2B ATP A1814 1555 1555 3.32 LINK CA CA A 404 O3A ATP A1814 1555 1555 2.74 LINK CA CA A 404 OD1 ASP A 105 1555 1555 2.70 LINK CA CA A 404 O HOH A1932 1555 1555 2.43 LINK CA CA A 404 O HOH A1963 1555 1555 2.84 LINK CA CA A 404 O HOH A1816 1555 1555 2.21 LINK CA CA A 404 OD2 ASP A 105 1555 1555 2.87 CISPEP 1 LYS A 159 PRO A 160 0 0.38 SITE 1 AC1 6 ASP A 7 PHE A 8 ASP A 105 ATP A1814 SITE 2 AC1 6 HOH A1821 HOH A1959 SITE 1 AC2 5 ASP A 105 ATP A1814 HOH A1816 HOH A1932 SITE 2 AC2 5 HOH A1963 SITE 1 AC3 19 ASP A 7 TYR A 10 PHE A 11 ALA A 44 SITE 2 AC3 19 THR A 45 ARG A 51 ASP A 105 LYS A 159 SITE 3 AC3 19 CA A 402 CA A 404 HOH A1820 HOH A1821 SITE 4 AC3 19 HOH A1826 HOH A1910 HOH A1959 HOH A1969 SITE 5 AC3 19 DC B1813 DT C1905 DG C1906 CRYST1 98.519 101.556 52.246 90.00 90.00 90.00 P 21 21 2 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010150 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019140 0.00000 MASTER 416 0 3 16 12 0 9 6 0 0 0 31 END