HEADER HYDROLASE 04-JUN-14 4TNO TITLE HYPOTHETICAL PROTEIN PF1117 FROM PYROCOCCUS FURIOSUS: STRUCTURE SOLVED TITLE 2 BY SULFUR-SAD USING SWISS LIGHT SOURCE DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS2; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS FURIOSUS; SOURCE 3 ORGANISM_TAXID: 186497; SOURCE 4 STRAIN: ATCC 43587 / DSM 3638 / JCM 8422 / VC1; SOURCE 5 GENE: CAS2, PF1117; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SULFUR SAD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.WEINERT,S.WALTERSPERGER,V.OLIERIC,E.PANEPUCCI,L.CHEN,J.P.ROSE, AUTHOR 2 M.WANG,B.C.WANG,SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS AUTHOR 3 (SECSG) REVDAT 6 27-DEC-23 4TNO 1 REMARK REVDAT 5 22-NOV-17 4TNO 1 REMARK REVDAT 4 12-AUG-15 4TNO 1 JRNL REVDAT 3 11-FEB-15 4TNO 1 JRNL REVDAT 2 14-JAN-15 4TNO 1 JRNL REVDAT 1 10-DEC-14 4TNO 0 JRNL AUTH T.WEINERT,V.OLIERIC,S.WALTERSPERGER,E.PANEPUCCI,L.CHEN, JRNL AUTH 2 H.ZHANG,D.ZHOU,J.ROSE,A.EBIHARA,S.KURAMITSU,D.LI,N.HOWE, JRNL AUTH 3 G.SCHNAPP,A.PAUTSCH,K.BARGSTEN,A.E.PROTA,P.SURANA,J.KOTTUR, JRNL AUTH 4 D.T.NAIR,F.BASILICO,V.CECATIELLO,S.PASQUALATO,A.BOLAND, JRNL AUTH 5 O.WEICHENRIEDER,B.C.WANG,M.O.STEINMETZ,M.CAFFREY,M.WANG JRNL TITL FAST NATIVE-SAD PHASING FOR ROUTINE MACROMOLECULAR STRUCTURE JRNL TITL 2 DETERMINATION. JRNL REF NAT.METHODS V. 12 131 2015 JRNL REFN ESSN 1548-7105 JRNL PMID 25506719 JRNL DOI 10.1038/NMETH.3211 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 9591 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.258 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.830 REMARK 3 FREE R VALUE TEST SET COUNT : 943 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 40.9559 - 4.0816 1.00 1287 130 0.2078 0.2426 REMARK 3 2 4.0816 - 3.2401 1.00 1275 140 0.2486 0.2943 REMARK 3 3 3.2401 - 2.8307 1.00 1267 150 0.2970 0.3240 REMARK 3 4 2.8307 - 2.5719 1.00 1246 144 0.3405 0.5124 REMARK 3 5 2.5719 - 2.3876 1.00 1271 146 0.3265 0.3676 REMARK 3 6 2.3876 - 2.2468 1.00 1272 127 0.3033 0.4208 REMARK 3 7 2.2468 - 2.1400 0.80 1030 106 0.3301 0.3956 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 0.386 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.010 704 REMARK 3 ANGLE : 1.338 947 REMARK 3 CHIRALITY : 0.050 108 REMARK 3 PLANARITY : 0.009 119 REMARK 3 DIHEDRAL : 19.321 276 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 4TNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000201938. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 2.066 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10426 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.140 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 (%) : 97.1 REMARK 200 DATA REDUNDANCY : 76.20 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 71.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 65.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE, SHELXCD, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MICROLITER DROPS CONTAINING EQUAL REMARK 280 VOLUMES OF PROTEIN SOLUTION (10 MG/ML) AND A PRECIPITANT REMARK 280 SOLUTION CONTAINING 0.1M SODIUM CITRATE BUFFER CONTAINING 0.1 M REMARK 280 CHES, PH 7.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 41.14000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.60500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.60500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 20.57000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.60500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.60500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.71000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.60500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.60500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 20.57000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.60500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.60500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 61.71000 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 41.14000 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: 3510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 41.14000 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 ILE A 85 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN A 29 O HOH A 201 1.94 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 56 -13.16 -178.25 REMARK 500 SER A 57 -5.12 -145.66 REMARK 500 ILE A 76 99.95 -57.45 REMARK 500 ASN A 79 88.19 -153.56 REMARK 500 PRO A 80 135.59 -36.78 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 CL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I0X RELATED DB: PDB REMARK 900 PDB ENTRY 2I0X WAS SOLVED BY SE-SAD. THIS ENTRY WAS SOLVED BY S-SAD REMARK 900 USING DATA COLLECTED AT THE SWISS LIGHT SOURCE DBREF 4TNO A 1 85 UNP Q8U1T8 CAS2_PYRFU 1 85 SEQRES 1 A 85 MET TYR ILE VAL VAL VAL TYR ASP VAL GLY VAL GLU ARG SEQRES 2 A 85 VAL ASN LYS VAL LYS LYS PHE LEU ARG MET HIS LEU ASN SEQRES 3 A 85 TRP VAL GLN ASN SER VAL PHE GLU GLY GLU VAL THR LEU SEQRES 4 A 85 ALA GLU PHE GLU ARG ILE LYS GLU GLY LEU LYS LYS ILE SEQRES 5 A 85 ILE ASP GLU ASN SER ASP SER VAL ILE ILE TYR LYS LEU SEQRES 6 A 85 ARG SER MET PRO PRO ARG GLU THR LEU GLY ILE GLU LYS SEQRES 7 A 85 ASN PRO ILE GLU GLU ILE ILE HET CL A 101 1 HET CL A 102 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 2(CL 1-) FORMUL 4 HOH *9(H2 O) HELIX 1 AA1 ARG A 13 ARG A 22 1 10 HELIX 2 AA2 THR A 38 ILE A 53 1 16 SHEET 1 AA1 4 ASN A 26 GLN A 29 0 SHEET 2 AA1 4 VAL A 32 GLU A 36 -1 O GLU A 34 N ASN A 26 SHEET 3 AA1 4 TYR A 2 ASP A 8 -1 N VAL A 5 O PHE A 33 SHEET 4 AA1 4 SER A 59 LEU A 65 -1 O TYR A 63 N VAL A 4 SITE 1 AC1 4 ARG A 22 TRP A 27 HOH A 207 HOH A 208 SITE 1 AC2 4 LYS A 19 ARG A 22 GLU A 36 MET A 68 CRYST1 47.210 47.210 82.280 90.00 90.00 90.00 P 41 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 0.021182 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012154 0.00000