PDB Short entry for 1RC8 HEADER TRANSFERASE/DNA 03-NOV-03 1RC8 TITLE T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-GTCAC-3' SSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*TP*CP*AP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: POLYNUCLEOTIDE KINASE; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: PNK, POLYNUCLEOTIDE 5'-HYDROXYL- KINASE; COMPND 9 EC: 2.7.1.78; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 5 ORGANISM_TAXID: 10665; SOURCE 6 GENE: PSET; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PALL17 KEYWDS KINASE, PHOSPHATASE, ALPHA/BETA, P-LOOP, SSDNA, TRANSFERASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.H.EASTBERG,J.PELLETIER,B.L.STODDARD REVDAT 3 23-AUG-23 1RC8 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1RC8 1 VERSN REVDAT 1 17-FEB-04 1RC8 0 JRNL AUTH J.H.EASTBERG,J.PELLETIER,B.L.STODDARD JRNL TITL RECOGNITION OF DNA SUBSTRATES BY T4 BACTERIOPHAGE JRNL TITL 2 POLYNUCLEOTIDE KINASE. JRNL REF NUCLEIC ACIDS RES. V. 32 653 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 14754987 JRNL DOI 10.1093/NAR/GKH212 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 161032.550 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 10827 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) : 0.230 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1112 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1493 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 12.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2297 REMARK 3 NUCLEIC ACID ATOMS : 58 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.80000 REMARK 3 B22 (A**2) : 7.46000 REMARK 3 B33 (A**2) : -5.67000 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) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.46 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) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.62 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 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) : 6.470 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 10.030; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.910 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 11.460; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 50.49 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-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : LIGAND.PARAM REMARK 3 PARAMETER FILE 5 : ION.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : LIGAND.TOP REMARK 3 TOPOLOGY FILE 4 : WATER.TOP REMARK 3 TOPOLOGY FILE 5 : ION.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RC8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-03. REMARK 100 THE DEPOSITION ID IS D_1000020648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11117 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.1 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1LTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, POTASSIUM CHLORIDE, MES, REMARK 280 TRIS, ATP, DTT, EDTA, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 41.08500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.03050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.69250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.08500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.03050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 61.69250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.08500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.03050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.69250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.08500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.03050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.69250 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: OCTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 -1.000000 0.000000 0.000000 164.34000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 184.12200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 164.34000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 123.38500 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 184.12200 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 123.38500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 536 LIES ON A SPECIAL POSITION. 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 DA B 403 REMARK 465 DC B 404 REMARK 465 ASN A 174 REMARK 465 GLY A 175 REMARK 465 ARG A 176 REMARK 465 GLY A 177 REMARK 465 PRO A 178 REMARK 465 TYR A 179 REMARK 465 ASP A 180 REMARK 465 LEU A 181 REMARK 465 GLU A 182 REMARK 465 LYS A 183 REMARK 465 CYS A 184 REMARK 465 ASP A 185 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 GLU A 46 CG CD OE1 OE2 REMARK 470 ARG A 47 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 49 CG CD OE1 OE2 REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 GLU A 91 CG CD OE1 OE2 REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LYS A 230 CG CD CE NZ REMARK 470 LYS A 264 CG CD CE NZ 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 PHE A 22 -72.77 -57.09 REMARK 500 ASN A 26 61.13 -109.80 REMARK 500 ASP A 76 14.33 -62.57 REMARK 500 SER A 84 42.73 -72.44 REMARK 500 ASN A 87 28.46 44.77 REMARK 500 GLU A 102 43.42 -84.14 REMARK 500 TYR A 103 -13.85 -159.09 REMARK 500 LYS A 158 155.00 -45.18 REMARK 500 VAL A 166 -67.36 -104.26 REMARK 500 THR A 169 -69.66 -106.88 REMARK 500 PRO A 191 -78.75 -28.68 REMARK 500 LEU A 202 -73.74 -59.82 REMARK 500 MSE A 203 -56.19 -21.82 REMARK 500 LYS A 218 -60.43 -28.72 REMARK 500 PRO A 221 4.55 -55.00 REMARK 500 LEU A 240 179.07 -58.83 REMARK 500 ASP A 255 -72.26 -41.21 REMARK 500 ILE A 266 -64.61 -103.65 REMARK 500 LEU A 274 152.61 176.98 REMARK 500 ASP A 278 -30.04 -138.47 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 ADP A 900 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 700 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 165 OD1 REMARK 620 2 ASP A 167 O 74.0 REMARK 620 3 ASP A 278 OD1 78.9 78.5 REMARK 620 4 HOH A 516 O 76.3 139.3 122.0 REMARK 620 5 HOH A 517 O 131.2 57.4 87.3 145.7 REMARK 620 6 HOH A 518 O 119.8 94.7 157.9 76.7 71.5 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 CA A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RPZ RELATED DB: PDB REMARK 900 T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-TGCAC-3' SSDNA REMARK 900 RELATED ID: 1RRC RELATED DB: PDB REMARK 900 T4 POLYNUCLEOTIDE KINASE BOUND TO 5'-GTC-3' SSDNA' DBREF 1RC8 A 1 301 UNP P06855 KIPN_BPT4 1 301 DBREF 1RC8 B 400 404 PDB 1RC8 1RC8 400 404 SEQADV 1RC8 MSE A 1 UNP P06855 MET 1 MODIFIED RESIDUE SEQADV 1RC8 MSE A 42 UNP P06855 MET 42 MODIFIED RESIDUE SEQADV 1RC8 MSE A 63 UNP P06855 MET 63 MODIFIED RESIDUE SEQADV 1RC8 MSE A 139 UNP P06855 MET 139 MODIFIED RESIDUE SEQADV 1RC8 MSE A 143 UNP P06855 MET 143 MODIFIED RESIDUE SEQADV 1RC8 MSE A 173 UNP P06855 MET 173 MODIFIED RESIDUE SEQADV 1RC8 MSE A 192 UNP P06855 MET 192 MODIFIED RESIDUE SEQADV 1RC8 MSE A 199 UNP P06855 MET 199 MODIFIED RESIDUE SEQADV 1RC8 MSE A 203 UNP P06855 MET 203 MODIFIED RESIDUE SEQADV 1RC8 MSE A 227 UNP P06855 MET 227 MODIFIED RESIDUE SEQADV 1RC8 MSE A 242 UNP P06855 MET 242 MODIFIED RESIDUE SEQADV 1RC8 MSE A 285 UNP P06855 MET 285 MODIFIED RESIDUE SEQRES 1 B 5 DG DT DC DA DC SEQRES 1 A 301 MSE LYS LYS ILE ILE LEU THR ILE GLY CYS PRO GLY SER SEQRES 2 A 301 GLY LYS SER THR TRP ALA ARG GLU PHE ILE ALA LYS ASN SEQRES 3 A 301 PRO GLY PHE TYR ASN ILE ASN ARG ASP ASP TYR ARG GLN SEQRES 4 A 301 SER ILE MSE ALA HIS GLU GLU ARG ASP GLU TYR LYS TYR SEQRES 5 A 301 THR LYS LYS LYS GLU GLY ILE VAL THR GLY MSE GLN PHE SEQRES 6 A 301 ASP THR ALA LYS SER ILE LEU TYR GLY GLY ASP SER VAL SEQRES 7 A 301 LYS GLY VAL ILE ILE SER ASP THR ASN LEU ASN PRO GLU SEQRES 8 A 301 ARG ARG LEU ALA TRP GLU THR PHE ALA LYS GLU TYR GLY SEQRES 9 A 301 TRP LYS VAL GLU HIS LYS VAL PHE ASP VAL PRO TRP THR SEQRES 10 A 301 GLU LEU VAL LYS ARG ASN SER LYS ARG GLY THR LYS ALA SEQRES 11 A 301 VAL PRO ILE ASP VAL LEU ARG SER MSE TYR LYS SER MSE SEQRES 12 A 301 ARG GLU TYR LEU GLY LEU PRO VAL TYR ASN GLY THR PRO SEQRES 13 A 301 GLY LYS PRO LYS ALA VAL ILE PHE ASP VAL ASP GLY THR SEQRES 14 A 301 LEU ALA LYS MSE ASN GLY ARG GLY PRO TYR ASP LEU GLU SEQRES 15 A 301 LYS CYS ASP THR ASP VAL ILE ASN PRO MSE VAL VAL GLU SEQRES 16 A 301 LEU SER LYS MSE TYR ALA LEU MSE GLY TYR GLN ILE VAL SEQRES 17 A 301 VAL VAL SER GLY ARG GLU SER GLY THR LYS GLU ASP PRO SEQRES 18 A 301 THR LYS TYR TYR ARG MSE THR ARG LYS TRP VAL GLU ASP SEQRES 19 A 301 ILE ALA GLY VAL PRO LEU VAL MSE GLN CYS GLN ARG GLU SEQRES 20 A 301 GLN GLY ASP THR ARG LYS ASP ASP VAL VAL LYS GLU GLU SEQRES 21 A 301 ILE PHE TRP LYS HIS ILE ALA PRO HIS PHE ASP VAL LYS SEQRES 22 A 301 LEU ALA ILE ASP ASP ARG THR GLN VAL VAL GLU MSE TRP SEQRES 23 A 301 ARG ARG ILE GLY VAL GLU CYS TRP GLN VAL ALA SER GLY SEQRES 24 A 301 ASP PHE MODRES 1RC8 MSE A 1 MET SELENOMETHIONINE MODRES 1RC8 MSE A 42 MET SELENOMETHIONINE MODRES 1RC8 MSE A 63 MET SELENOMETHIONINE MODRES 1RC8 MSE A 139 MET SELENOMETHIONINE MODRES 1RC8 MSE A 143 MET SELENOMETHIONINE MODRES 1RC8 MSE A 173 MET SELENOMETHIONINE MODRES 1RC8 MSE A 192 MET SELENOMETHIONINE MODRES 1RC8 MSE A 199 MET SELENOMETHIONINE MODRES 1RC8 MSE A 203 MET SELENOMETHIONINE MODRES 1RC8 MSE A 227 MET SELENOMETHIONINE MODRES 1RC8 MSE A 242 MET SELENOMETHIONINE MODRES 1RC8 MSE A 285 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 42 8 HET MSE A 63 8 HET MSE A 139 8 HET MSE A 143 8 HET MSE A 173 8 HET MSE A 192 8 HET MSE A 199 8 HET MSE A 203 8 HET MSE A 227 8 HET MSE A 242 8 HET MSE A 285 8 HET CA A 700 1 HET DMS A 800 4 HET ADP A 900 17 HETNAM MSE SELENOMETHIONINE HETNAM CA CALCIUM ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 2 MSE 12(C5 H11 N O2 SE) FORMUL 3 CA CA 2+ FORMUL 4 DMS C2 H6 O S FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 HOH *59(H2 O) HELIX 1 1 GLY A 14 ASN A 26 1 13 HELIX 2 2 ASN A 33 ILE A 41 1 9 HELIX 3 3 THR A 53 TYR A 73 1 21 HELIX 4 4 ASN A 89 GLU A 102 1 14 HELIX 5 5 PRO A 115 LYS A 125 1 11 HELIX 6 6 ARG A 126 ALA A 130 5 5 HELIX 7 7 PRO A 132 GLY A 148 1 17 HELIX 8 8 ASN A 190 GLY A 204 1 15 HELIX 9 9 THR A 222 ILE A 235 1 14 HELIX 10 10 LYS A 253 ILE A 266 1 14 HELIX 11 11 ARG A 279 ILE A 289 1 11 SHEET 1 A 4 PHE A 29 ILE A 32 0 SHEET 2 A 4 GLY A 80 ILE A 83 1 O ILE A 82 N TYR A 30 SHEET 3 A 4 LYS A 3 ILE A 8 1 N ILE A 5 O ILE A 83 SHEET 4 A 4 LYS A 106 VAL A 111 1 O GLU A 108 N LEU A 6 SHEET 1 B 5 MSE A 242 ARG A 246 0 SHEET 2 B 5 GLN A 206 GLU A 214 1 N VAL A 209 O MSE A 242 SHEET 3 B 5 LYS A 160 ASP A 165 1 N PHE A 164 O VAL A 210 SHEET 4 B 5 ASP A 271 ASP A 277 1 O LYS A 273 N ALA A 161 SHEET 5 B 5 CYS A 293 GLN A 295 1 O TRP A 294 N ALA A 275 SHEET 1 C 2 ALA A 171 LYS A 172 0 SHEET 2 C 2 VAL A 188 ILE A 189 -1 O VAL A 188 N LYS A 172 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C ILE A 41 N MSE A 42 1555 1555 1.33 LINK C MSE A 42 N ALA A 43 1555 1555 1.33 LINK C GLY A 62 N MSE A 63 1555 1555 1.33 LINK C MSE A 63 N GLN A 64 1555 1555 1.33 LINK C SER A 138 N MSE A 139 1555 1555 1.33 LINK C MSE A 139 N TYR A 140 1555 1555 1.33 LINK C SER A 142 N MSE A 143 1555 1555 1.33 LINK C MSE A 143 N ARG A 144 1555 1555 1.33 LINK C LYS A 172 N MSE A 173 1555 1555 1.33 LINK C PRO A 191 N MSE A 192 1555 1555 1.33 LINK C MSE A 192 N VAL A 193 1555 1555 1.33 LINK C LYS A 198 N MSE A 199 1555 1555 1.34 LINK C MSE A 199 N TYR A 200 1555 1555 1.33 LINK C LEU A 202 N MSE A 203 1555 1555 1.33 LINK C MSE A 203 N GLY A 204 1555 1555 1.33 LINK C ARG A 226 N MSE A 227 1555 1555 1.33 LINK C MSE A 227 N THR A 228 1555 1555 1.33 LINK C VAL A 241 N MSE A 242 1555 1555 1.32 LINK C MSE A 242 N GLN A 243 1555 1555 1.33 LINK C GLU A 284 N MSE A 285 1555 1555 1.33 LINK C MSE A 285 N TRP A 286 1555 1555 1.33 LINK OD1 ASP A 165 CA CA A 700 1555 1555 2.38 LINK O ASP A 167 CA CA A 700 1555 1555 2.42 LINK OD1 ASP A 278 CA CA A 700 1555 1555 2.59 LINK O HOH A 516 CA CA A 700 1555 1555 3.12 LINK O HOH A 517 CA CA A 700 1555 1555 2.76 LINK O HOH A 518 CA CA A 700 1555 1555 2.71 SITE 1 AC1 5 ASP A 165 ASP A 167 ASP A 278 HOH A 517 SITE 2 AC1 5 HOH A 518 SITE 1 AC2 3 HIS A 109 ARG A 226 HOH A 512 SITE 1 AC3 10 PRO A 11 GLY A 12 SER A 13 GLY A 14 SITE 2 AC3 10 LYS A 15 SER A 16 THR A 17 GLU A 45 SITE 3 AC3 10 ARG A 126 LYS A 129 CRYST1 82.170 92.061 123.385 90.00 90.00 90.00 I 2 2 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 0.012170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010862 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008105 0.00000