PDB Short entry for 3H8J HEADER HYDROLASE 29-APR-09 3H8J TITLE NATIVE T4 RNASE H IN THE ABSENCE OF DIVALENT METAL IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_COMMON: BACTERIOPHAGE T4; SOURCE 4 ORGANISM_TAXID: 10665; SOURCE 5 STRAIN: T4D; SOURCE 6 GENE: 33.2, DAS, RNH; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PNN2202 KEYWDS HYDROLASE, BPT4 RNASE H, 5'-3' EXONUCLEASE, ENDONUCLEASE, NUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR S.J.TOMANICEK,T.C.MUESER REVDAT 2 06-SEP-23 3H8J 1 REMARK REVDAT 1 12-MAY-10 3H8J 0 JRNL AUTH S.J.TOMANICEK,J.M.DEVOS,T.C.MUESER JRNL TITL ADDITIONAL ORDER APPEARS IN THE ABSENCE OF METALS IN A FEN-1 JRNL TITL 2 PROTEIN: STRUCTURAL ANALYSIS OF MAGNESIUM BINDING TO JRNL TITL 3 BACTERIOPHAGE T4 RNASEH JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 32304 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.150 REMARK 3 FREE R VALUE TEST SET COUNT : 1017 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.2542 - 3.4377 1.00 4606 162 0.1709 0.1731 REMARK 3 2 3.4377 - 2.7311 1.00 4542 160 0.2029 0.2283 REMARK 3 3 2.7311 - 2.3866 1.00 4535 158 0.2041 0.2648 REMARK 3 4 2.3866 - 2.1687 0.98 4450 141 0.1944 0.1892 REMARK 3 5 2.1687 - 2.0134 0.98 4518 127 0.2015 0.2526 REMARK 3 6 2.0134 - 1.8948 0.98 4460 132 0.1941 0.2391 REMARK 3 7 1.8948 - 1.8000 0.92 4176 137 0.1908 0.1954 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 36.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3H8J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052826. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL 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 : 33128 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1TFR NATIVE T4 RNASE H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 300 MM AMMONIUM ACETATE, 100 MM SODIUM REMARK 280 CACODYLATE, 15% PEG 8000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.22900 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 LEU A 3 REMARK 465 GLU A 4 REMARK 465 MET A 5 REMARK 465 MET A 6 REMARK 465 LEU A 7 REMARK 465 ASP A 8 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 SER A 97 149.67 -34.17 REMARK 500 PRO A 120 40.89 -86.71 REMARK 500 LYS A 128 6.84 82.87 REMARK 500 REMARK 500 REMARK: NULL 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 NA A 306 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 115 O REMARK 620 2 MET A 119 O 74.9 REMARK 620 3 TYR A 121 O 123.7 85.7 REMARK 620 4 TYR A 278 OH 113.8 162.3 76.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H7I RELATED DB: PDB REMARK 900 METAL-FREE D132N T4 RNASE H REMARK 900 RELATED ID: 1TFR RELATED DB: PDB REMARK 900 RNASE H FROM BACTERIOPHAGE T4 REMARK 900 RELATED ID: 2IHN RELATED DB: PDB REMARK 900 CO-CRYSTAL OF BACTERIOPHAGE T4 RNASE H WITH A FORK DNA SUBSTRATE REMARK 900 RELATED ID: 3H8S RELATED DB: PDB REMARK 900 RELATED ID: 3H8W RELATED DB: PDB DBREF 3H8J A 1 305 UNP P13319 RNH_BPT4 1 305 SEQRES 1 A 305 MET ASP LEU GLU MET MET LEU ASP GLU ASP TYR LYS GLU SEQRES 2 A 305 GLY ILE CYS LEU ILE ASP PHE SER GLN ILE ALA LEU SER SEQRES 3 A 305 THR ALA LEU VAL ASN PHE PRO ASP LYS GLU LYS ILE ASN SEQRES 4 A 305 LEU SER MET VAL ARG HIS LEU ILE LEU ASN SER ILE LYS SEQRES 5 A 305 PHE ASN VAL LYS LYS ALA LYS THR LEU GLY TYR THR LYS SEQRES 6 A 305 ILE VAL LEU CYS ILE ASP ASN ALA LYS SER GLY TYR TRP SEQRES 7 A 305 ARG ARG ASP PHE ALA TYR TYR TYR LYS LYS ASN ARG GLY SEQRES 8 A 305 LYS ALA ARG GLU GLU SER THR TRP ASP TRP GLU GLY TYR SEQRES 9 A 305 PHE GLU SER SER HIS LYS VAL ILE ASP GLU LEU LYS ALA SEQRES 10 A 305 TYR MET PRO TYR ILE VAL MET ASP ILE ASP LYS TYR GLU SEQRES 11 A 305 ALA ASP ASP HIS ILE ALA VAL LEU VAL LYS LYS PHE SER SEQRES 12 A 305 LEU GLU GLY HIS LYS ILE LEU ILE ILE SER SER ASP GLY SEQRES 13 A 305 ASP PHE THR GLN LEU HIS LYS TYR PRO ASN VAL LYS GLN SEQRES 14 A 305 TRP SER PRO MET HIS LYS LYS TRP VAL LYS ILE LYS SER SEQRES 15 A 305 GLY SER ALA GLU ILE ASP CYS MET THR LYS ILE LEU LYS SEQRES 16 A 305 GLY ASP LYS LYS ASP ASN VAL ALA SER VAL LYS VAL ARG SEQRES 17 A 305 SER ASP PHE TRP PHE THR ARG VAL GLU GLY GLU ARG THR SEQRES 18 A 305 PRO SER MET LYS THR SER ILE VAL GLU ALA ILE ALA ASN SEQRES 19 A 305 ASP ARG GLU GLN ALA LYS VAL LEU LEU THR GLU SER GLU SEQRES 20 A 305 TYR ASN ARG TYR LYS GLU ASN LEU VAL LEU ILE ASP PHE SEQRES 21 A 305 ASP TYR ILE PRO ASP ASN ILE ALA SER ASN ILE VAL ASN SEQRES 22 A 305 TYR TYR ASN SER TYR LYS LEU PRO PRO ARG GLY LYS ILE SEQRES 23 A 305 TYR SER TYR PHE VAL LYS ALA GLY LEU SER LYS LEU THR SEQRES 24 A 305 ASN SER ILE ASN GLU PHE HET NA A 306 1 HET SO4 A 307 5 HETNAM NA SODIUM ION HETNAM SO4 SULFATE ION FORMUL 2 NA NA 1+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *282(H2 O) HELIX 1 1 PHE A 20 PHE A 32 1 13 HELIX 2 2 ASN A 39 GLY A 62 1 24 HELIX 3 3 TYR A 77 ALA A 83 1 7 HELIX 4 4 LYS A 87 SER A 97 1 11 HELIX 5 5 ASP A 100 MET A 119 1 20 HELIX 6 6 GLU A 130 GLU A 145 1 16 HELIX 7 7 PHE A 158 HIS A 162 5 5 HELIX 8 8 SER A 184 GLY A 196 1 13 HELIX 9 9 ASP A 197 ASN A 201 5 5 HELIX 10 10 ASP A 210 ARG A 215 1 6 HELIX 11 11 LYS A 225 ASP A 235 1 11 HELIX 12 12 GLN A 238 LEU A 243 1 6 HELIX 13 13 THR A 244 ASP A 259 1 16 HELIX 14 14 PHE A 260 ILE A 263 5 4 HELIX 15 15 PRO A 264 SER A 277 1 14 HELIX 16 16 GLY A 284 ALA A 293 1 10 HELIX 17 17 SER A 301 PHE A 305 5 5 SHEET 1 A 6 ILE A 122 MET A 124 0 SHEET 2 A 6 LYS A 65 CYS A 69 1 N LEU A 68 O MET A 124 SHEET 3 A 6 ILE A 15 ASP A 19 1 N CYS A 16 O LYS A 65 SHEET 4 A 6 ILE A 149 ILE A 152 1 O ILE A 152 N ASP A 19 SHEET 5 A 6 VAL A 167 SER A 171 1 O LYS A 168 N ILE A 151 SHEET 6 A 6 LYS A 176 VAL A 178 -1 O VAL A 178 N GLN A 169 LINK O LEU A 115 NA NA A 306 1555 1555 2.95 LINK O MET A 119 NA NA A 306 1555 1555 2.86 LINK O TYR A 121 NA NA A 306 1555 1555 2.87 LINK OH TYR A 278 NA NA A 306 1555 1555 2.69 SITE 1 AC1 6 LEU A 115 LYS A 116 MET A 119 TYR A 121 SITE 2 AC1 6 TYR A 278 PRO A 281 SITE 1 AC2 4 ARG A 215 GLU A 217 GLY A 218 ARG A 220 CRYST1 36.257 86.458 57.796 90.00 92.04 90.00 P 1 21 1 2 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 0.027581 0.000000 0.000981 0.00000 SCALE2 0.000000 0.011566 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017313 0.00000