HEADER HYDROLASE 17-MAY-07 2JPN TITLE SOLUTION STRUCTURE OF T4 BACTERIOPHAGE HELICASE UVSW.1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT DNA HELICASE UVSW; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES, 512-587; COMPND 5 SYNONYM: DAR PROTEIN; COMPND 6 EC: 3.6.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 GENE: UVSW, DAR; 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: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS UVSW, BACTERIOPHAGE HELICASE, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.G.SIVAKOLUNDU,T.LEE,S.W.WHITE,R.W.KRIWACKI REVDAT 6 20-DEC-23 2JPN 1 REMARK REVDAT 5 09-MAR-22 2JPN 1 REMARK SEQADV REVDAT 4 24-FEB-09 2JPN 1 VERSN REVDAT 3 18-DEC-07 2JPN 1 JRNL REVDAT 2 30-OCT-07 2JPN 1 JRNL REVDAT 1 10-JUL-07 2JPN 0 JRNL AUTH I.D.KERR,S.SIVAKOLUNDU,Z.LI,J.C.BUCHSBAUM,L.A.KNOX, JRNL AUTH 2 R.KRIWACKI,S.W.WHITE JRNL TITL CRYSTALLOGRAPHIC AND NMR ANALYSES OF UVSW AND UVSW.1 FROM JRNL TITL 2 BACTERIOPHAGE T4 JRNL REF J.BIOL.CHEM. V. 282 34392 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17878153 JRNL DOI 10.1074/JBC.M705900200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, AMBER 9 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CASE, DARDEN, CHEATHAM, III, SIMMERLING, REMARK 3 WANG, DUKE, LUO, AND KOLL (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ARIA 1.2 WAS USED TO CALCULATE 100 REMARK 3 STRUCTURES. AMBER 9 WAS USED TO REFINE 20 LOW ENERGY STRUCTURES REMARK 3 USING GBSA SOLVATION METHOD. REMARK 4 REMARK 4 2JPN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000100131. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.66 MM [U-99% 13C; U-99% 15N] REMARK 210 UVSW.1, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 3D C(CO)NH; 3D REMARK 210 H(CCO)NH; 3D HCCH-COSY; 3D 1H- REMARK 210 13C NOESY; 3D 1H-15N NOESY; 3D REMARK 210 HCCH-TOCSY; 2D 1H-15N HSQC, REMARK 210 STEADY STATE {1H}-15N NOE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, ARIA 1.2, REMARK 210 PROCHECKNMR, TALOS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 1 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 TYR A 40 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 3 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ILE A 24 CA - CB - CG1 ANGL. DEV. = 12.3 DEGREES REMARK 500 5 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 LEU A 36 CB - CG - CD1 ANGL. DEV. = 11.1 DEGREES REMARK 500 7 TYR A 40 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 7 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 LEU A 36 CB - CG - CD1 ANGL. DEV. = 11.8 DEGREES REMARK 500 8 LEU A 49 CB - CG - CD1 ANGL. DEV. = 11.0 DEGREES REMARK 500 8 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 LYS A 23 CB - CA - C ANGL. DEV. = 14.8 DEGREES REMARK 500 9 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 TYR A 40 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 12 LEU A 36 CB - CG - CD1 ANGL. DEV. = 11.2 DEGREES REMARK 500 12 VAL A 44 CA - CB - CG1 ANGL. DEV. = 9.6 DEGREES REMARK 500 13 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 13 VAL A 44 CA - CB - CG1 ANGL. DEV. = 9.5 DEGREES REMARK 500 13 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ILE A 24 CA - CB - CG1 ANGL. DEV. = 12.4 DEGREES REMARK 500 14 THR A 52 CA - CB - CG2 ANGL. DEV. = 10.7 DEGREES REMARK 500 14 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 LYS A 23 CB - CA - C ANGL. DEV. = 13.4 DEGREES REMARK 500 15 ARG A 43 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 15 VAL A 57 CA - CB - CG2 ANGL. DEV. = 11.0 DEGREES REMARK 500 15 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 LEU A 49 CB - CG - CD1 ANGL. DEV. = 10.4 DEGREES REMARK 500 17 ILE A 24 CA - CB - CG1 ANGL. DEV. = 12.1 DEGREES REMARK 500 17 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ILE A 24 CA - CB - CG1 ANGL. DEV. = 12.0 DEGREES REMARK 500 18 LEU A 49 CB - CG - CD1 ANGL. DEV. = 12.3 DEGREES REMARK 500 18 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 LEU A 36 CB - CG - CD1 ANGL. DEV. = 11.5 DEGREES REMARK 500 19 TYR A 40 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 20 ARG A 65 NE - CZ - NH1 ANGL. DEV. = 3.3 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 1 LEU A 6 -21.04 63.44 REMARK 500 1 GLN A 28 -5.93 61.51 REMARK 500 1 THR A 47 -143.81 -144.21 REMARK 500 1 LEU A 49 2.97 53.84 REMARK 500 1 LYS A 50 -165.17 39.71 REMARK 500 1 ASP A 73 52.48 -58.91 REMARK 500 1 GLU A 76 -35.56 60.18 REMARK 500 1 SER A 78 11.48 -148.05 REMARK 500 2 MET A 4 -169.33 56.74 REMARK 500 2 LEU A 6 110.83 -32.89 REMARK 500 2 GLU A 19 -59.60 -130.45 REMARK 500 2 GLN A 28 -6.91 58.97 REMARK 500 2 THR A 47 114.45 48.54 REMARK 500 2 LEU A 49 85.76 -67.02 REMARK 500 2 ASP A 72 18.59 42.15 REMARK 500 2 GLU A 76 -28.61 -152.78 REMARK 500 3 SER A 2 -21.93 62.43 REMARK 500 3 GLU A 19 -41.35 -133.30 REMARK 500 3 GLN A 28 -5.97 58.57 REMARK 500 3 THR A 47 -133.04 -150.37 REMARK 500 3 LEU A 49 91.78 -64.43 REMARK 500 3 LYS A 50 167.91 -48.40 REMARK 500 3 ASP A 73 123.37 -39.31 REMARK 500 3 VAL A 75 -55.67 54.96 REMARK 500 3 GLU A 76 -27.96 -145.45 REMARK 500 3 GLU A 77 -56.93 -163.97 REMARK 500 3 SER A 78 17.00 -165.00 REMARK 500 4 MET A 4 -178.80 62.00 REMARK 500 4 LEU A 6 -32.56 -150.93 REMARK 500 4 GLU A 19 -63.57 -132.71 REMARK 500 4 GLN A 28 -6.11 63.12 REMARK 500 4 THR A 47 -152.02 -153.84 REMARK 500 4 VAL A 75 -53.69 59.60 REMARK 500 4 GLU A 76 -28.98 -147.56 REMARK 500 4 GLU A 77 -55.78 -165.39 REMARK 500 4 SER A 78 26.88 -169.63 REMARK 500 5 MET A 4 169.05 55.95 REMARK 500 5 GLU A 19 -38.69 -134.29 REMARK 500 5 GLN A 28 -6.77 61.13 REMARK 500 5 THR A 47 -153.63 -129.46 REMARK 500 5 GLU A 76 -37.59 64.00 REMARK 500 5 SER A 78 50.38 -141.79 REMARK 500 6 PHE A 8 -19.26 66.57 REMARK 500 6 GLU A 19 -54.20 -134.13 REMARK 500 6 GLN A 28 -3.74 61.63 REMARK 500 6 THR A 47 -152.68 -142.54 REMARK 500 6 GLU A 76 -21.30 59.91 REMARK 500 7 LEU A 6 105.31 62.77 REMARK 500 7 PHE A 8 -17.12 48.10 REMARK 500 7 THR A 47 -123.04 -144.17 REMARK 500 REMARK 500 THIS ENTRY HAS 162 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 9 GLN A 10 1 -145.99 REMARK 500 ARG A 43 VAL A 44 1 -149.38 REMARK 500 THR A 47 GLU A 48 2 140.32 REMARK 500 ASP A 73 GLU A 74 5 -148.82 REMARK 500 GLU A 48 LEU A 49 8 -143.49 REMARK 500 THR A 47 GLU A 48 10 -149.57 REMARK 500 ASP A 73 GLU A 74 10 -141.04 REMARK 500 THR A 47 GLU A 48 11 -149.08 REMARK 500 GLU A 48 LEU A 49 14 -149.28 REMARK 500 THR A 47 GLU A 48 15 136.54 REMARK 500 GLU A 48 LEU A 49 16 -148.61 REMARK 500 ASP A 73 GLU A 74 17 133.81 REMARK 500 THR A 47 GLU A 48 20 -149.06 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 3 TYR A 39 0.08 SIDE CHAIN REMARK 500 5 TYR A 13 0.07 SIDE CHAIN REMARK 500 7 PHE A 20 0.08 SIDE CHAIN REMARK 500 8 TYR A 40 0.11 SIDE CHAIN REMARK 500 9 TYR A 13 0.07 SIDE CHAIN REMARK 500 9 TYR A 39 0.10 SIDE CHAIN REMARK 500 10 TYR A 13 0.09 SIDE CHAIN REMARK 500 10 TYR A 39 0.07 SIDE CHAIN REMARK 500 11 TYR A 39 0.07 SIDE CHAIN REMARK 500 14 TYR A 13 0.08 SIDE CHAIN REMARK 500 14 TYR A 39 0.08 SIDE CHAIN REMARK 500 14 TYR A 40 0.07 SIDE CHAIN REMARK 500 15 TYR A 39 0.10 SIDE CHAIN REMARK 500 16 TYR A 39 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2JPN A 4 79 UNP P20703 UVSW_BPT4 512 587 SEQADV 2JPN GLY A 1 UNP P20703 CLONING ARTIFACT SEQADV 2JPN SER A 2 UNP P20703 CLONING ARTIFACT SEQADV 2JPN HIS A 3 UNP P20703 CLONING ARTIFACT SEQRES 1 A 79 GLY SER HIS MET LEU LEU GLU PHE LYS GLN PHE LEU TYR SEQRES 2 A 79 GLU ALA SER ILE ASP GLU PHE MET GLY LYS ILE ALA SER SEQRES 3 A 79 CYS GLN THR LEU GLU GLY LEU GLU GLU LEU GLU ALA TYR SEQRES 4 A 79 TYR LYS LYS ARG VAL LYS GLU THR GLU LEU LYS ASP THR SEQRES 5 A 79 ASP ASP ILE SER VAL ARG ASP ALA LEU ALA GLY LYS ARG SEQRES 6 A 79 ALA GLU LEU GLU ASP SER ASP ASP GLU VAL GLU GLU SER SEQRES 7 A 79 PHE HELIX 1 1 LYS A 9 SER A 16 1 8 HELIX 2 2 GLU A 19 SER A 26 1 8 HELIX 3 3 THR A 29 VAL A 44 1 16 HELIX 4 4 ASP A 51 SER A 71 1 21 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1