HEADER HYDROLASE 06-OCT-16 5H0O TITLE CRYSTAL STRUCTURE OF DEEP-SEA THERMOPHILIC BACTERIOPHAGE GVE2 HNH TITLE 2 ENDONUCLEASE WITH MANGANESE ION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HNH ENDONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS VIRUS E2; SOURCE 3 ORGANISM_TAXID: 447909; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS THERMOPHILIC BACTERIOPHAGE, HNH ENDONUCLEASE, DNA NICKING, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.K.ZHANG,D.D.XU,Y.C.HUANG,Y.GONG REVDAT 3 08-NOV-23 5H0O 1 REMARK REVDAT 2 26-FEB-20 5H0O 1 REMARK REVDAT 1 08-MAR-17 5H0O 0 JRNL AUTH L.K.ZHANG,D.D.XU,Y.C.HUANG,X.Y.ZHU,M.W.RUI,T.WAN,X.ZHENG, JRNL AUTH 2 Y.L.SHEN,X.D.CHEN,K.S.MA,Y.GONG JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF DEEP-SEA JRNL TITL 2 THERMOPHILIC BACTERIOPHAGE GVE2 HNH ENDONUCLEASE. JRNL REF SCI REP V. 7 42542 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28211904 JRNL DOI 10.1038/SREP42542 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11_2567: ???) 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 922 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 25.8597 - 2.9256 0.99 2606 124 0.1513 0.1604 REMARK 3 2 2.9256 - 2.3226 1.00 2508 117 0.1521 0.1746 REMARK 3 3 2.3226 - 2.0291 1.00 2441 142 0.1265 0.1861 REMARK 3 4 2.0291 - 1.8437 1.00 2433 127 0.1285 0.1770 REMARK 3 5 1.8437 - 1.7116 1.00 2416 139 0.1205 0.1716 REMARK 3 6 1.7116 - 1.6107 1.00 2395 143 0.1226 0.1861 REMARK 3 7 1.6107 - 1.5300 1.00 2421 130 0.1374 0.1951 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 794 REMARK 3 ANGLE : 0.961 1065 REMARK 3 CHIRALITY : 0.057 111 REMARK 3 PLANARITY : 0.005 138 REMARK 3 DIHEDRAL : 20.161 311 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 5H0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001801. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19106 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.40 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5H0M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 0.2M SODIUM CHLORIDE, PH REMARK 280 7.5, 25% (W/V) POLYETHYLENE GLYCOL 4000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 25.75550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.42350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.42350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.63325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.42350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.42350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 12.87775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.42350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.42350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 38.63325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.42350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.42350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 12.87775 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 25.75550 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 PRO A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 PRO A 5 REMARK 465 LEU A 6 REMARK 465 ARG A 7 REMARK 465 PRO A 8 REMARK 465 CYS A 9 REMARK 465 ASN A 10 REMARK 465 LYS A 11 REMARK 465 ILE A 12 REMARK 465 GLY A 13 REMARK 465 CYS A 14 REMARK 465 THR A 15 REMARK 465 ASN A 16 REMARK 465 LEU A 17 REMARK 465 THR A 18 REMARK 465 ARG A 19 REMARK 465 ASP A 20 REMARK 465 ARG A 21 REMARK 465 TYR A 22 REMARK 465 CYS A 23 REMARK 465 GLU A 24 REMARK 465 GLN A 25 REMARK 465 HIS A 26 REMARK 465 LYS A 27 REMARK 465 HIS A 28 REMARK 465 LEU A 29 REMARK 465 ALA A 30 REMARK 465 GLU A 31 REMARK 465 GLN A 32 REMARK 465 ARG A 33 REMARK 465 GLN A 34 REMARK 465 ARG A 35 REMARK 465 THR A 36 REMARK 465 ARG A 37 REMARK 465 ARG A 38 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 489 DISTANCE = 6.64 ANGSTROMS REMARK 525 HOH A 490 DISTANCE = 6.86 ANGSTROMS 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 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 76 SG REMARK 620 2 CYS A 79 SG 112.3 REMARK 620 3 CYS A 114 SG 112.2 113.5 REMARK 620 4 CYS A 117 SG 104.1 112.3 101.6 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 MN A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H0M RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH ZN2+ REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE HAS BEEN DEPOSITED TO DATABASE WITH ACCESSION NUMBER REMARK 999 YP_001522898.1. DBREF 5H0O A 1 130 PDB 5H0O 5H0O 1 130 SEQRES 1 A 130 MET PRO SER LYS PRO LEU ARG PRO CYS ASN LYS ILE GLY SEQRES 2 A 130 CYS THR ASN LEU THR ARG ASP ARG TYR CYS GLU GLN HIS SEQRES 3 A 130 LYS HIS LEU ALA GLU GLN ARG GLN ARG THR ARG ARG ASN SEQRES 4 A 130 ASP LYS GLU TYR ASP LYS HIS LYS ARG ASN GLN GLN ALA SEQRES 5 A 130 ARG ALA PHE TYR HIS SER ARG GLU TRP GLU ARG THR ARG SEQRES 6 A 130 LEU ALA VAL LEU ALA LYS ASP ASN TYR LEU CYS GLN HIS SEQRES 7 A 130 CYS LEU LYS GLU LYS LYS ILE THR ARG ALA VAL ILE VAL SEQRES 8 A 130 ASP HIS ILE THR PRO LEU LEU VAL ASP TRP SER LYS ARG SEQRES 9 A 130 LEU ASP MET ASP ASN LEU GLN SER LEU CYS GLN ALA CYS SEQRES 10 A 130 HIS ASN ARG LYS THR ALA GLU ASP LYS ARG ARG TYR GLY HET MN A 201 1 HETNAM MN MANGANESE (II) ION FORMUL 2 MN MN 2+ FORMUL 3 HOH *190(H2 O) HELIX 1 AA1 ASP A 40 TYR A 56 1 17 HELIX 2 AA2 SER A 58 ASP A 72 1 15 HELIX 3 AA3 CYS A 76 GLU A 82 1 7 HELIX 4 AA4 ASP A 100 ARG A 104 5 5 HELIX 5 AA5 ASP A 106 ASP A 108 5 3 HELIX 6 AA6 CYS A 114 GLY A 130 1 17 SHEET 1 AA1 2 ILE A 90 HIS A 93 0 SHEET 2 AA1 2 LEU A 110 LEU A 113 -1 O LEU A 113 N ILE A 90 LINK SG CYS A 76 MN MN A 201 1555 1555 2.33 LINK SG CYS A 79 MN MN A 201 1555 1555 2.32 LINK SG CYS A 114 MN MN A 201 1555 1555 2.32 LINK SG CYS A 117 MN MN A 201 1555 1555 2.33 SITE 1 AC1 4 CYS A 76 CYS A 79 CYS A 114 CYS A 117 CRYST1 66.847 66.847 51.511 90.00 90.00 90.00 P 43 21 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 0.014960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019413 0.00000