HEADER LIGASE 22-JAN-04 1S68 TITLE STRUCTURE AND MECHANISM OF RNA LIGASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA LIGASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (RESIDUES 1-249); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 GENE: Y10A, 24.1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS RIBONUCLEIC ACID LIGASE, RNA REPAIR, T4, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR C.K.HO,L.K.WANG,C.D.LIMA,S.SHUMAN REVDAT 3 14-FEB-24 1S68 1 REMARK REVDAT 2 24-FEB-09 1S68 1 VERSN REVDAT 1 24-FEB-04 1S68 0 JRNL AUTH C.K.HO,L.K.WANG,C.D.LIMA,S.SHUMAN JRNL TITL STRUCTURE AND MECHANISM OF RNA LIGASE. JRNL REF STRUCTURE V. 12 327 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 14962393 JRNL DOI 10.1016/S0969-2126(04)00023-1 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1235118.630 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 19459 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) : 0.190 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2710 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE : 0.2940 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1865 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.03000 REMARK 3 B22 (A**2) : 6.06000 REMARK 3 B33 (A**2) : -3.03000 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) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 1.320 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.090 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.540 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.640 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 48.89 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 : ION.PARAM REMARK 3 PARAMETER FILE 5 : AMP_XPLOR.PAR 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 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : AMP_XPLOR.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1S68 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021418. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-03; 15-MAY-03 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; NSLS REMARK 200 BEAMLINE : NULL; X4A REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.9790 REMARK 200 MONOCHROMATOR : OSMIC MULTILAYER; SAGITALLY REMARK 200 FOCUSED SI(111) REMARK 200 OPTICS : OSMIC; SAG FOCUS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV; ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19766 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS, 8.5, 0.2M SODIUM ACETATE, REMARK 280 5MM DTT, 28% PEG-3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 296K, PH 8.5 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 28.85850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.94600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.85850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.94600 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: 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 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 348 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 539 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 LYS A 234 REMARK 465 LYS A 235 REMARK 465 LYS A 236 REMARK 465 SER A 237 REMARK 465 ASP A 238 REMARK 465 LYS A 239 REMARK 465 PRO A 240 REMARK 465 ILE A 241 REMARK 465 LYS A 242 REMARK 465 ALA A 243 REMARK 465 LYS A 244 REMARK 465 VAL A 245 REMARK 465 GLU A 246 REMARK 465 LEU A 247 REMARK 465 SER A 248 REMARK 465 GLU A 249 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 ILE A 105 -76.33 -81.64 REMARK 500 CYS A 112 -158.69 67.37 REMARK 500 PHE A 201 123.14 -29.61 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 AMP A 301 DBREF 1S68 A 1 249 UNP P32277 Y10A_BPT4 1 249 SEQRES 1 A 249 MET PHE LYS LYS TYR SER SER LEU GLU ASN HIS TYR ASN SEQRES 2 A 249 SER LYS PHE ILE GLU LYS LEU TYR SER LEU GLY LEU THR SEQRES 3 A 249 GLY GLY GLU TRP VAL ALA ARG GLU LYS ILE HIS GLY THR SEQRES 4 A 249 ASN PHE SER LEU ILE ILE GLU ARG ASP LYS VAL THR CYS SEQRES 5 A 249 ALA LYS ARG THR GLY PRO ILE LEU PRO ALA GLU ASP PHE SEQRES 6 A 249 PHE GLY TYR GLU ILE ILE LEU LYS ASN TYR ALA ASP SER SEQRES 7 A 249 ILE LYS ALA VAL GLN ASP ILE MET GLU THR SER ALA VAL SEQRES 8 A 249 VAL SER TYR GLN VAL PHE GLY GLU PHE ALA GLY PRO GLY SEQRES 9 A 249 ILE GLN LYS ASN VAL ASP TYR CYS ASP LYS ASP PHE TYR SEQRES 10 A 249 VAL PHE ASP ILE ILE VAL THR THR GLU SER GLY ASP VAL SEQRES 11 A 249 THR TYR VAL ASP ASP TYR MET MET GLU SER PHE CYS ASN SEQRES 12 A 249 THR PHE LYS PHE LYS MET ALA PRO LEU LEU GLY ARG GLY SEQRES 13 A 249 LYS PHE GLU GLU LEU ILE LYS LEU PRO ASN ASP LEU ASP SEQRES 14 A 249 SER VAL VAL GLN ASP TYR ASN PHE THR VAL ASP HIS ALA SEQRES 15 A 249 GLY LEU VAL ASP ALA ASN LYS CYS VAL TRP ASN ALA GLU SEQRES 16 A 249 ALA LYS GLY GLU VAL PHE THR ALA GLU GLY TYR VAL LEU SEQRES 17 A 249 LYS PRO CYS TYR PRO SER TRP LEU ARG ASN GLY ASN ARG SEQRES 18 A 249 VAL ALA ILE LYS CYS LYS ASN SER LYS PHE SER GLU LYS SEQRES 19 A 249 LYS LYS SER ASP LYS PRO ILE LYS ALA LYS VAL GLU LEU SEQRES 20 A 249 SER GLU HET AMP A 301 23 HETNAM AMP ADENOSINE MONOPHOSPHATE FORMUL 2 AMP C10 H14 N5 O7 P FORMUL 3 HOH *242(H2 O) HELIX 1 1 ASN A 13 GLY A 24 1 12 HELIX 2 2 TYR A 68 TYR A 75 1 8 HELIX 3 3 TYR A 75 ALA A 90 1 16 HELIX 4 4 ASP A 134 LYS A 146 1 13 HELIX 5 5 LYS A 157 ILE A 162 1 6 HELIX 6 6 VAL A 171 GLY A 183 1 13 HELIX 7 7 GLY A 183 CYS A 190 1 8 HELIX 8 8 SER A 229 SER A 232 5 4 SHEET 1 A 5 GLU A 9 ASN A 10 0 SHEET 2 A 5 ILE A 224 LYS A 227 1 O LYS A 225 N GLU A 9 SHEET 3 A 5 GLY A 205 PRO A 210 -1 N TYR A 206 O CYS A 226 SHEET 4 A 5 TRP A 30 GLU A 34 -1 N VAL A 31 O LYS A 209 SHEET 5 A 5 LEU A 152 GLY A 156 -1 O GLY A 156 N TRP A 30 SHEET 1 B 6 GLY A 57 PRO A 58 0 SHEET 2 B 6 VAL A 50 LYS A 54 -1 N LYS A 54 O GLY A 57 SHEET 3 B 6 THR A 39 GLU A 46 -1 N ILE A 44 O THR A 51 SHEET 4 B 6 VAL A 91 ALA A 101 -1 O TYR A 94 N ILE A 45 SHEET 5 B 6 ASP A 115 THR A 125 -1 O ILE A 122 N GLN A 95 SHEET 6 B 6 VAL A 130 TYR A 132 -1 O THR A 131 N VAL A 123 SHEET 1 C 6 GLY A 57 PRO A 58 0 SHEET 2 C 6 VAL A 50 LYS A 54 -1 N LYS A 54 O GLY A 57 SHEET 3 C 6 THR A 39 GLU A 46 -1 N ILE A 44 O THR A 51 SHEET 4 C 6 VAL A 91 ALA A 101 -1 O TYR A 94 N ILE A 45 SHEET 5 C 6 ASP A 115 THR A 125 -1 O ILE A 122 N GLN A 95 SHEET 6 C 6 LYS A 148 MET A 149 1 O LYS A 148 N VAL A 118 SITE 1 AC1 14 TYR A 5 GLU A 34 LYS A 35 ILE A 36 SITE 2 AC1 14 ASN A 40 ARG A 55 GLU A 99 PHE A 119 SITE 3 AC1 14 ALA A 150 VAL A 207 LYS A 225 LYS A 227 SITE 4 AC1 14 HOH A 317 HOH A 355 CRYST1 57.717 89.892 47.737 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 0.017326 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020948 0.00000