PDB Short entry for 2HVR HEADER LIGASE/RNA/DNA 30-JUL-06 2HVR TITLE STRUCTURE OF T4 RNA LIGASE 2 WITH NICKED 5'-ADENYLATED NUCLEIC ACID TITLE 2 DUPLEX CONTAINING A 3'-DEOXYRIBONUCLEOTIDE AT THE NICK COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*GP*GP*GP*TP*CP*GP COMPND 3 *CP*AP*AP*TP*TP*G)-3'; COMPND 4 CHAIN: C, F; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*AP*AP*TP*TP*GP*CP*GP*AP*C)-R(P*(OMC)P*C)-3'; COMPND 8 CHAIN: D, G; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'-R(P*A)-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*T)-3'; COMPND 12 CHAIN: E, H; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: T4 RNA LIGASE 2; COMPND 16 CHAIN: A, B; COMPND 17 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 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 9 ORGANISM_TAXID: 10665; SOURCE 10 GENE: Y10A, 24.1; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PET-HIS-SMT3-RNL2 KEYWDS RNA, LIGASE, LYSINE ADENYLATE, T4, PROTEIN DNA-RNA COMPLEX, LIGASE- KEYWDS 2 RNA-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.NANDAKUMAR,C.D.LIMA REVDAT 3 30-AUG-23 2HVR 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2HVR 1 VERSN REVDAT 1 17-OCT-06 2HVR 0 JRNL AUTH J.NANDAKUMAR,S.SHUMAN,C.D.LIMA JRNL TITL RNA LIGASE STRUCTURES REVEAL THE BASIS FOR RNA SPECIFICITY JRNL TITL 2 AND CONFORMATIONAL CHANGES THAT DRIVE LIGATION FORWARD. JRNL REF CELL(CAMBRIDGE,MASS.) V. 127 71 2006 JRNL REFN ISSN 0092-8674 JRNL PMID 17018278 JRNL DOI 10.1016/J.CELL.2006.08.038 REMARK 2 REMARK 2 RESOLUTION. 2.45 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 234106.953 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 41156 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) : 0.236 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2056 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.60 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6329 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE : 0.3780 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 348 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5042 REMARK 3 NUCLEIC ACID ATOMS : 2006 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.03000 REMARK 3 B22 (A**2) : 9.12000 REMARK 3 B33 (A**2) : 3.90000 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) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.51 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) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.53 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.980 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) : 2.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.710 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.690 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.720 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.26 REMARK 3 BSOL : 27.82 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : BTB.PARAM REMARK 3 PARAMETER FILE 5 : DNA-RNA-APC_REP.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : BTB.TOP REMARK 3 TOPOLOGY FILE 5 : DNA-RNA-APC.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HVR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000038819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-05 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41212 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.37200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2HVQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS, 22% PEG-4000, 9% PEG REMARK 280 -6000, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 41.78450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.66450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.08000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.66450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.78450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.08000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: ASYMMETRIC UNIT CONTAINS TWO COMPLEXES OF T4 RNA LIGASE 2 REMARK 300 COMPLEXED WITH NICKED DUPLEX RELATED BY A NON-CRYSTALLOGRAPHIC REMARK 300 PSEUDO-TRANSLATION ALONG THE X-AXIS. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, E, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, G, H, B 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 SER A 232 REMARK 465 GLU A 233 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 VAL A 333 REMARK 465 SER A 334 REMARK 465 PHE B 231 REMARK 465 SER B 232 REMARK 465 GLU B 233 REMARK 465 LYS B 234 REMARK 465 LYS B 235 REMARK 465 LYS B 236 REMARK 465 SER B 237 REMARK 465 ASP B 238 REMARK 465 LYS B 239 REMARK 465 PRO B 240 REMARK 465 ILE B 241 REMARK 465 LYS B 242 REMARK 465 ALA B 243 REMARK 465 LYS B 244 REMARK 465 VAL B 245 REMARK 465 GLU B 246 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 PHE A 231 CG CD1 CD2 CE1 CE2 CZ 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 A E 236 C2 A E 236 N3 0.063 REMARK 500 A E 236 N3 A E 236 C4 0.055 REMARK 500 A E 236 C5 A E 236 N7 -0.038 REMARK 500 A H 236 N1 A H 236 C2 0.062 REMARK 500 A H 236 C2 A H 236 N3 0.065 REMARK 500 A H 236 N3 A H 236 C4 0.062 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 A E 236 N1 - C2 - N3 ANGL. DEV. = -8.5 DEGREES REMARK 500 A E 236 C2 - N3 - C4 ANGL. DEV. = 9.9 DEGREES REMARK 500 A E 236 N3 - C4 - C5 ANGL. DEV. = -7.8 DEGREES REMARK 500 A E 236 C4 - C5 - C6 ANGL. DEV. = 3.1 DEGREES REMARK 500 A E 236 C4 - C5 - N7 ANGL. DEV. = -3.4 DEGREES REMARK 500 A E 236 C5 - N7 - C8 ANGL. DEV. = 4.9 DEGREES REMARK 500 A E 236 N7 - C8 - N9 ANGL. DEV. = -3.7 DEGREES REMARK 500 A E 236 N3 - C4 - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 A H 236 N1 - C2 - N3 ANGL. DEV. = -8.3 DEGREES REMARK 500 A H 236 C2 - N3 - C4 ANGL. DEV. = 9.8 DEGREES REMARK 500 A H 236 N3 - C4 - C5 ANGL. DEV. = -7.8 DEGREES REMARK 500 A H 236 C4 - C5 - C6 ANGL. DEV. = 3.3 DEGREES REMARK 500 A H 236 C4 - C5 - N7 ANGL. DEV. = -3.4 DEGREES REMARK 500 A H 236 C5 - N7 - C8 ANGL. DEV. = 5.2 DEGREES REMARK 500 A H 236 N7 - C8 - N9 ANGL. DEV. = -3.9 DEGREES REMARK 500 A H 236 N3 - C4 - N9 ANGL. DEV. = 6.4 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 ASN A 13 85.91 -61.18 REMARK 500 LYS A 54 -169.11 -102.72 REMARK 500 PHE A 66 19.51 54.64 REMARK 500 PRO A 151 123.42 -30.39 REMARK 500 ILE A 162 -5.66 -59.96 REMARK 500 LEU A 164 132.12 -35.81 REMARK 500 HIS A 181 -83.85 -136.83 REMARK 500 PRO A 213 130.66 -34.25 REMARK 500 ALA A 250 -84.76 -68.04 REMARK 500 ASN A 252 -1.92 -56.36 REMARK 500 LYS A 273 38.00 -80.33 REMARK 500 GLU A 276 87.96 -64.40 REMARK 500 ILE A 277 55.87 -100.12 REMARK 500 ILE A 302 89.29 -53.91 REMARK 500 ALA A 307 147.37 -39.35 REMARK 500 ASP A 308 39.03 -92.37 REMARK 500 ASN A 309 51.89 155.92 REMARK 500 ILE A 313 -73.62 -59.18 REMARK 500 PRO A 327 -2.03 -52.34 REMARK 500 ALA A 328 21.70 -146.05 REMARK 500 GLU A 331 40.65 -77.01 REMARK 500 THR B 26 -4.89 -47.23 REMARK 500 LYS B 54 -161.90 -104.17 REMARK 500 ASN B 108 10.40 59.95 REMARK 500 TYR B 111 41.26 -109.98 REMARK 500 PHE B 119 -4.16 -140.70 REMARK 500 ASP B 120 149.01 -171.36 REMARK 500 ALA B 196 62.32 -100.07 REMARK 500 LYS B 197 -124.69 -80.28 REMARK 500 PRO B 213 66.99 -43.97 REMARK 500 ARG B 217 -30.98 -35.05 REMARK 500 ASN B 218 6.90 -60.43 REMARK 500 ALA B 250 -11.29 159.58 REMARK 500 ILE B 274 53.25 -151.47 REMARK 500 PRO B 279 17.10 -65.01 REMARK 500 VAL B 285 -70.05 -62.62 REMARK 500 GLU B 295 -71.34 -62.99 REMARK 500 ARG B 299 -9.05 -52.83 REMARK 500 ILE B 302 73.15 -117.92 REMARK 500 LEU B 304 31.13 -97.70 REMARK 500 THR B 305 41.39 -105.73 REMARK 500 ASP B 308 140.43 -31.54 REMARK 500 PRO B 310 16.15 -59.98 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 DG C 14 0.07 SIDE CHAIN REMARK 500 DA D 133 0.06 SIDE CHAIN REMARK 500 DC D 134 0.09 SIDE CHAIN REMARK 500 DG F 14 0.07 SIDE CHAIN REMARK 500 DG F 15 0.06 SIDE CHAIN REMARK 500 DA G 133 0.06 SIDE CHAIN REMARK 500 DC G 134 0.07 SIDE CHAIN 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 BTB C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTB F 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BTB A 335 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HVQ RELATED DB: PDB REMARK 900 STRUCTURE OF ADENYLATED FULL-LENGTH T4 RNA LIGASE 2 REMARK 900 RELATED ID: 2HVS RELATED DB: PDB REMARK 900 STRUCTURE OF T4 RNA LIGASE 2 WITH NICKED 5'-ADENYLATED NUCLEIC ACID REMARK 900 DUPLEX CONTAINING A 2'-DEOXYRIBONUCLEOTIDE AT THE NICK REMARK 999 REMARK 999 SEQUENCE REMARK 999 ACCORDING TO AUTHORS, GLYCINE AT POSITION 112 IS CORRECT. REMARK 999 THIS MUTATION LIKELY REPRESENTS A NATURAL MUTATION IN THE REMARK 999 'POPULATION' OF T4 PHAGE DBREF 2HVR A 1 334 UNP P32277 Y10A_BPT4 1 334 DBREF 2HVR B 1 334 UNP P32277 Y10A_BPT4 1 334 DBREF 2HVR C 1 24 PDB 2HVR 2HVR 1 24 DBREF 2HVR D 125 136 PDB 2HVR 2HVR 125 136 DBREF 2HVR E 236 248 PDB 2HVR 2HVR 236 248 DBREF 2HVR F 1 24 PDB 2HVR 2HVR 1 24 DBREF 2HVR G 125 136 PDB 2HVR 2HVR 125 136 DBREF 2HVR H 236 248 PDB 2HVR 2HVR 236 248 SEQADV 2HVR SER A 0 UNP P32277 CLONING ARTIFACT SEQADV 2HVR GLY A 112 UNP P32277 CYS 112 SEE REMARK 999 SEQADV 2HVR SER B 0 UNP P32277 CLONING ARTIFACT SEQADV 2HVR GLY B 112 UNP P32277 CYS 112 SEE REMARK 999 SEQRES 1 C 24 DA DT DT DC DC DG DA DT DA DG DT DG DG SEQRES 2 C 24 DG DG DT DC DG DC DA DA DT DT DG SEQRES 1 D 12 DC DA DA DT DT DG DC DG DA DC OMC O2C SEQRES 1 E 13 A DC DA DC DT DA DT DC DG DG DA DA DT SEQRES 1 F 24 DA DT DT DC DC DG DA DT DA DG DT DG DG SEQRES 2 F 24 DG DG DT DC DG DC DA DA DT DT DG SEQRES 1 G 12 DC DA DA DT DT DG DC DG DA DC OMC O2C SEQRES 1 H 13 A DC DA DC DT DA DT DC DG DG DA DA DT SEQRES 1 A 335 SER MET PHE LYS LYS TYR SER SER LEU GLU ASN HIS TYR SEQRES 2 A 335 ASN SER LYS PHE ILE GLU LYS LEU TYR SER LEU GLY LEU SEQRES 3 A 335 THR GLY GLY GLU TRP VAL ALA ARG GLU LYS ILE HIS GLY SEQRES 4 A 335 THR ASN PHE SER LEU ILE ILE GLU ARG ASP LYS VAL THR SEQRES 5 A 335 CYS ALA LYS ARG THR GLY PRO ILE LEU PRO ALA GLU ASP SEQRES 6 A 335 PHE PHE GLY TYR GLU ILE ILE LEU LYS ASN TYR ALA ASP SEQRES 7 A 335 SER ILE LYS ALA VAL GLN ASP ILE MET GLU THR SER ALA SEQRES 8 A 335 VAL VAL SER TYR GLN VAL PHE GLY GLU PHE ALA GLY PRO SEQRES 9 A 335 GLY ILE GLN LYS ASN VAL ASP TYR GLY ASP LYS ASP PHE SEQRES 10 A 335 TYR VAL PHE ASP ILE ILE VAL THR THR GLU SER GLY ASP SEQRES 11 A 335 VAL THR TYR VAL ASP ASP TYR MET MET GLU SER PHE CYS SEQRES 12 A 335 ASN THR PHE LYS PHE LYS MET ALA PRO LEU LEU GLY ARG SEQRES 13 A 335 GLY LYS PHE GLU GLU LEU ILE LYS LEU PRO ASN ASP LEU SEQRES 14 A 335 ASP SER VAL VAL GLN ASP TYR ASN PHE THR VAL ASP HIS SEQRES 15 A 335 ALA GLY LEU VAL ASP ALA ASN LYS CYS VAL TRP ASN ALA SEQRES 16 A 335 GLU ALA LYS GLY GLU VAL PHE THR ALA GLU GLY TYR VAL SEQRES 17 A 335 LEU LYS PRO CYS TYR PRO SER TRP LEU ARG ASN GLY ASN SEQRES 18 A 335 ARG VAL ALA ILE LYS CYS LYS ASN SER LYS PHE SER GLU SEQRES 19 A 335 LYS LYS LYS SER ASP LYS PRO ILE LYS ALA LYS VAL GLU SEQRES 20 A 335 LEU SER GLU ALA ASP ASN LYS LEU VAL GLY ILE LEU ALA SEQRES 21 A 335 CYS TYR VAL THR LEU ASN ARG VAL ASN ASN VAL ILE SER SEQRES 22 A 335 LYS ILE GLY GLU ILE GLY PRO LYS ASP PHE GLY LYS VAL SEQRES 23 A 335 MET GLY LEU THR VAL GLN ASP ILE LEU GLU GLU THR SER SEQRES 24 A 335 ARG GLU GLY ILE THR LEU THR GLN ALA ASP ASN PRO SER SEQRES 25 A 335 LEU ILE LYS LYS GLU LEU VAL LYS MET VAL GLN ASP VAL SEQRES 26 A 335 LEU ARG PRO ALA TRP ILE GLU LEU VAL SER SEQRES 1 B 335 SER MET PHE LYS LYS TYR SER SER LEU GLU ASN HIS TYR SEQRES 2 B 335 ASN SER LYS PHE ILE GLU LYS LEU TYR SER LEU GLY LEU SEQRES 3 B 335 THR GLY GLY GLU TRP VAL ALA ARG GLU LYS ILE HIS GLY SEQRES 4 B 335 THR ASN PHE SER LEU ILE ILE GLU ARG ASP LYS VAL THR SEQRES 5 B 335 CYS ALA LYS ARG THR GLY PRO ILE LEU PRO ALA GLU ASP SEQRES 6 B 335 PHE PHE GLY TYR GLU ILE ILE LEU LYS ASN TYR ALA ASP SEQRES 7 B 335 SER ILE LYS ALA VAL GLN ASP ILE MET GLU THR SER ALA SEQRES 8 B 335 VAL VAL SER TYR GLN VAL PHE GLY GLU PHE ALA GLY PRO SEQRES 9 B 335 GLY ILE GLN LYS ASN VAL ASP TYR GLY ASP LYS ASP PHE SEQRES 10 B 335 TYR VAL PHE ASP ILE ILE VAL THR THR GLU SER GLY ASP SEQRES 11 B 335 VAL THR TYR VAL ASP ASP TYR MET MET GLU SER PHE CYS SEQRES 12 B 335 ASN THR PHE LYS PHE LYS MET ALA PRO LEU LEU GLY ARG SEQRES 13 B 335 GLY LYS PHE GLU GLU LEU ILE LYS LEU PRO ASN ASP LEU SEQRES 14 B 335 ASP SER VAL VAL GLN ASP TYR ASN PHE THR VAL ASP HIS SEQRES 15 B 335 ALA GLY LEU VAL ASP ALA ASN LYS CYS VAL TRP ASN ALA SEQRES 16 B 335 GLU ALA LYS GLY GLU VAL PHE THR ALA GLU GLY TYR VAL SEQRES 17 B 335 LEU LYS PRO CYS TYR PRO SER TRP LEU ARG ASN GLY ASN SEQRES 18 B 335 ARG VAL ALA ILE LYS CYS LYS ASN SER LYS PHE SER GLU SEQRES 19 B 335 LYS LYS LYS SER ASP LYS PRO ILE LYS ALA LYS VAL GLU SEQRES 20 B 335 LEU SER GLU ALA ASP ASN LYS LEU VAL GLY ILE LEU ALA SEQRES 21 B 335 CYS TYR VAL THR LEU ASN ARG VAL ASN ASN VAL ILE SER SEQRES 22 B 335 LYS ILE GLY GLU ILE GLY PRO LYS ASP PHE GLY LYS VAL SEQRES 23 B 335 MET GLY LEU THR VAL GLN ASP ILE LEU GLU GLU THR SER SEQRES 24 B 335 ARG GLU GLY ILE THR LEU THR GLN ALA ASP ASN PRO SER SEQRES 25 B 335 LEU ILE LYS LYS GLU LEU VAL LYS MET VAL GLN ASP VAL SEQRES 26 B 335 LEU ARG PRO ALA TRP ILE GLU LEU VAL SER MODRES 2HVR OMC D 135 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 2HVR OMC G 135 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HET OMC D 135 21 HET O2C D 136 19 HET OMC G 135 21 HET O2C G 136 19 HET BTB C 201 14 HET BTB F 202 14 HET BTB A 335 14 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM O2C 3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETSYN BTB BIS-TRIS BUFFER FORMUL 2 OMC 2(C10 H16 N3 O8 P) FORMUL 2 O2C 2(C9 H14 N3 O7 P) FORMUL 9 BTB 3(C8 H19 N O5) FORMUL 12 HOH *129(H2 O) HELIX 1 1 ASN A 13 LEU A 23 1 11 HELIX 2 2 TYR A 68 TYR A 75 1 8 HELIX 3 3 TYR A 75 GLU A 87 1 13 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 ASP A 180 1 10 HELIX 7 7 GLY A 183 CYS A 190 1 8 HELIX 8 8 ASP A 251 ALA A 259 1 9 HELIX 9 9 CYS A 260 VAL A 262 5 3 HELIX 10 10 THR A 263 LYS A 273 1 11 HELIX 11 11 ASP A 281 GLU A 300 1 20 HELIX 12 12 ASN A 309 ARG A 326 1 18 HELIX 13 13 PRO A 327 TRP A 329 5 3 HELIX 14 14 ASN B 13 LEU B 23 1 11 HELIX 15 15 TYR B 68 ALA B 90 1 23 HELIX 16 16 ASP B 134 LYS B 146 1 13 HELIX 17 17 LYS B 157 ILE B 162 1 6 HELIX 18 18 VAL B 171 ALA B 182 1 12 HELIX 19 19 GLY B 183 CYS B 190 1 8 HELIX 20 20 ASN B 252 CYS B 260 1 9 HELIX 21 21 THR B 263 SER B 272 1 10 HELIX 22 22 ASP B 281 ARG B 299 1 19 HELIX 23 23 SER B 311 SER B 334 1 24 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 LEU A 208 O ILE A 224 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 LEU A 153 N ALA A 32 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 PHE A 100 N THR A 39 SHEET 5 B 6 ASP A 115 THR A 125 -1 O ASP A 120 N PHE A 97 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 PHE A 100 N THR A 39 SHEET 5 C 6 ASP A 115 THR A 125 -1 O ASP A 120 N PHE A 97 SHEET 6 C 6 LYS A 148 MET A 149 1 O LYS A 148 N VAL A 118 SHEET 1 D 5 GLU B 9 ASN B 10 0 SHEET 2 D 5 ILE B 224 LYS B 227 1 O LYS B 225 N GLU B 9 SHEET 3 D 5 GLY B 205 PRO B 210 -1 N LEU B 208 O ILE B 224 SHEET 4 D 5 TRP B 30 LYS B 35 -1 N VAL B 31 O LYS B 209 SHEET 5 D 5 LEU B 152 GLY B 154 -1 O LEU B 153 N ALA B 32 SHEET 1 E 5 VAL B 50 ALA B 53 0 SHEET 2 E 5 THR B 39 GLU B 46 -1 N ILE B 44 O THR B 51 SHEET 3 E 5 VAL B 91 ALA B 101 -1 O GLY B 98 N PHE B 41 SHEET 4 E 5 ASP B 115 THR B 125 -1 O ASP B 120 N PHE B 97 SHEET 5 E 5 VAL B 130 TYR B 132 -1 O THR B 131 N VAL B 123 SHEET 1 F 5 VAL B 50 ALA B 53 0 SHEET 2 F 5 THR B 39 GLU B 46 -1 N ILE B 44 O THR B 51 SHEET 3 F 5 VAL B 91 ALA B 101 -1 O GLY B 98 N PHE B 41 SHEET 4 F 5 ASP B 115 THR B 125 -1 O ASP B 120 N PHE B 97 SHEET 5 F 5 LYS B 148 MET B 149 1 O LYS B 148 N VAL B 118 SHEET 1 G 2 TRP B 215 LEU B 216 0 SHEET 2 G 2 ASN B 220 ARG B 221 -1 O ASN B 220 N LEU B 216 LINK O3' DC D 134 P OMC D 135 1555 1555 1.61 LINK O3' OMC D 135 P O2C D 136 1555 1555 1.59 LINK P A E 236 OP3 DC E 237 1555 1555 1.58 LINK O3' DC G 134 P OMC G 135 1555 1555 1.61 LINK O3' OMC G 135 P O2C G 136 1555 1555 1.59 LINK P A H 236 OP3 DC H 237 1555 1555 1.58 SITE 1 AC1 8 DT C 11 DG C 12 DG C 13 DG C 14 SITE 2 AC1 8 HOH C 128 DC D 134 OMC D 135 O2C D 136 SITE 1 AC2 6 DG F 12 DG F 13 DG F 14 DC G 134 SITE 2 AC2 6 OMC G 135 O2C G 136 SITE 1 AC3 6 ASN A 193 GLU A 195 LYS A 197 VAL B 130 SITE 2 AC3 6 THR B 131 TRP B 215 CRYST1 83.569 106.160 125.329 90.00 90.00 90.00 P 21 21 21 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 0.011966 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007979 0.00000