HEADER HYDROLASE 21-APR-12 4ES3 TITLE DOUBLE-STRANDED ENDONUCLEASE ACTIVITY IN B. HALODURANS CLUSTERED TITLE 2 REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS (CRISPR)-ASSOCIATED TITLE 3 CAS2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BH0342 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS HALODURANS; SOURCE 3 ORGANISM_TAXID: 272558; SOURCE 4 STRAIN: ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125; SOURCE 5 GENE: BH0342; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS FERREDOXIN, NUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KE,K.H.NAM REVDAT 4 28-FEB-24 4ES3 1 REMARK SEQADV REVDAT 3 28-NOV-18 4ES3 1 JRNL REVDAT 2 15-NOV-17 4ES3 1 REMARK REVDAT 1 22-AUG-12 4ES3 0 JRNL AUTH K.H.NAM,F.DING,C.HAITJEMA,Q.HUANG,M.P.DELISA,A.KE JRNL TITL DOUBLE-STRANDED ENDONUCLEASE ACTIVITY IN BACILLUS HALODURANS JRNL TITL 2 CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS JRNL TITL 3 (CRISPR)-ASSOCIATED CAS2 PROTEIN. JRNL REF J. BIOL. CHEM. V. 287 35943 2012 JRNL REFN ESSN 1083-351X JRNL PMID 22942283 JRNL DOI 10.1074/JBC.M112.382598 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.3_928 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.510 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 9507 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 951 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 15.0042 - 3.2506 0.97 1368 152 0.2021 0.2355 REMARK 3 2 3.2506 - 2.5844 0.99 1325 147 0.2055 0.2411 REMARK 3 3 2.5844 - 2.2589 0.94 1222 137 0.2154 0.2508 REMARK 3 4 2.2589 - 2.0530 0.94 1239 137 0.2188 0.2872 REMARK 3 5 2.0530 - 1.9061 0.93 1205 134 0.2225 0.2497 REMARK 3 6 1.9061 - 1.7939 0.86 1113 124 0.2198 0.2696 REMARK 3 7 1.7939 - 1.7040 0.84 1084 120 0.2539 0.2826 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 40.58 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.36950 REMARK 3 B22 (A**2) : -6.68210 REMARK 3 B33 (A**2) : 9.05160 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 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 : 0.008 678 REMARK 3 ANGLE : 1.027 905 REMARK 3 CHIRALITY : 0.074 108 REMARK 3 PLANARITY : 0.004 111 REMARK 3 DIHEDRAL : 15.961 261 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -8.6625 0.7688 -14.4096 REMARK 3 T TENSOR REMARK 3 T11: 0.1409 T22: 0.1435 REMARK 3 T33: 0.1283 T12: 0.0037 REMARK 3 T13: 0.0135 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.7614 L22: 1.4597 REMARK 3 L33: 0.6434 L12: -0.1237 REMARK 3 L13: 0.6500 L23: -0.2306 REMARK 3 S TENSOR REMARK 3 S11: 0.0060 S12: -0.1623 S13: -0.0646 REMARK 3 S21: 0.1008 S22: 0.0384 S23: 0.1999 REMARK 3 S31: 0.0757 S32: -0.1025 S33: 0.0008 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 4ES3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000071999. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9770 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9508 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 44.914 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.3 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 : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MES, PH 6.0, 4% W/V PEG6000, 10 REMARK 280 MM MAGNESIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 294K 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 26.30950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.95200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.30950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.95200 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 GLY A 72 REMARK 465 ASN A 73 REMARK 465 LYS A 76 REMARK 465 THR A 77 REMARK 465 SER A 87 REMARK 465 ILE A 88 REMARK 465 ASP A 89 REMARK 465 LEU A 90 REMARK 465 GLU A 91 REMARK 465 ASP A 92 REMARK 465 PRO A 93 REMARK 465 LEU A 94 REMARK 465 ILE A 95 REMARK 465 PHE A 96 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ES1 RELATED DB: PDB REMARK 900 RELATED ID: 4ES2 RELATED DB: PDB DBREF 4ES3 A 1 96 UNP Q9KFX8 Q9KFX8_BACHD 1 96 SEQADV 4ES3 GLY A -3 UNP Q9KFX8 EXPRESSION TAG SEQADV 4ES3 SER A -2 UNP Q9KFX8 EXPRESSION TAG SEQADV 4ES3 HIS A -1 UNP Q9KFX8 EXPRESSION TAG SEQADV 4ES3 MET A 0 UNP Q9KFX8 EXPRESSION TAG SEQRES 1 A 100 GLY SER HIS MET MET LEU VAL LEU ILE THR TYR ASP VAL SEQRES 2 A 100 GLN THR SER SER MET GLY GLY THR LYS ARG LEU ARG LYS SEQRES 3 A 100 VAL ALA LYS ALA CYS GLN ASN TYR GLY GLN ARG VAL GLN SEQRES 4 A 100 ASN SER VAL PHE GLU CYS ILE VAL ASP SER THR GLN LEU SEQRES 5 A 100 THR SER LEU LYS LEU GLU LEU THR SER LEU ILE ASP GLU SEQRES 6 A 100 GLU LYS ASP SER LEU ARG ILE TYR ARG LEU GLY ASN ASN SEQRES 7 A 100 TYR LYS THR LYS VAL GLU HIS ILE GLY ALA LYS PRO SER SEQRES 8 A 100 ILE ASP LEU GLU ASP PRO LEU ILE PHE HET EDO A 101 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 HOH *62(H2 O) HELIX 1 1 SER A 13 ASN A 29 1 17 HELIX 2 2 ASP A 44 ILE A 59 1 16 SHEET 1 A 4 GLY A 31 GLN A 35 0 SHEET 2 A 4 VAL A 38 VAL A 43 -1 O GLU A 40 N GLN A 32 SHEET 3 A 4 MET A 1 ASP A 8 -1 N MET A 1 O VAL A 43 SHEET 4 A 4 SER A 65 ARG A 70 -1 O SER A 65 N ASP A 8 SITE 1 AC1 6 GLU A 40 THR A 49 ARG A 67 HOH A 202 SITE 2 AC1 6 HOH A 211 HOH A 227 CRYST1 52.619 37.904 44.914 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 0.019005 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022265 0.00000