HEADER HYDROLASE 01-MAR-12 4DZD TITLE CRYSTAL STRUCTURE OF THE CRISPR-ASSOCIATED PROTEIN CAS6E FROM TITLE 2 ESCHERICHIA COLI STR. K-12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN YGCH; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAS6E; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YGCH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FERREDOXIN-LIKE DOMAIN, ENDORIBONUCLEASE, CRRNA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.WEI,G.HUANG,Y.WANG,W.GONG REVDAT 2 08-NOV-23 4DZD 1 REMARK SEQADV REVDAT 1 06-MAR-13 4DZD 0 JRNL AUTH J.WEI,G.HUANG,Y.WANG,W.GONG JRNL TITL CRYSTAL STRUCTURE OF ENDORIBONUCLEASE CAS6E FROM ESCHERICHIA JRNL TITL 2 COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16524 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 827 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 35.3818 - 3.6311 1.00 2774 170 0.2036 0.2390 REMARK 3 2 3.6311 - 2.8825 1.00 2649 132 0.1999 0.2674 REMARK 3 3 2.8825 - 2.5183 1.00 2604 128 0.2045 0.2319 REMARK 3 4 2.5183 - 2.2881 1.00 2591 126 0.1956 0.2584 REMARK 3 5 2.2881 - 2.1241 1.00 2578 119 0.1975 0.2139 REMARK 3 6 2.1241 - 1.9989 0.99 2501 152 0.2096 0.2601 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 : 0.36 REMARK 3 B_SOL : 41.47 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.12 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.51 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.72290 REMARK 3 B22 (A**2) : 2.72290 REMARK 3 B33 (A**2) : -5.44570 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 : 0.006 1594 REMARK 3 ANGLE : 0.986 2161 REMARK 3 CHIRALITY : 0.069 243 REMARK 3 PLANARITY : 0.004 279 REMARK 3 DIHEDRAL : 15.371 610 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 4DZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000070973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16585 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.999 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 21.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10000 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) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1WJ9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, 0.2M AMMONIUM ACETATE, REMARK 280 25% PEG3350, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289K 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 64.33000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.95000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.95000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.16500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.95000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.95000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 96.49500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.95000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.95000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.16500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.95000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.95000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 96.49500 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 64.33000 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 -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 SER A -8 REMARK 465 SER A -7 REMARK 465 GLY A -6 REMARK 465 LEU A -5 REMARK 465 VAL A -4 REMARK 465 PRO A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 ARG A 30 REMARK 465 PRO A 31 REMARK 465 ASP A 32 REMARK 465 ALA A 33 REMARK 465 ALA A 34 REMARK 465 ARG A 35 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 201 DBREF 4DZD A 1 199 UNP Q46897 YGCH_ECOLI 1 199 SEQADV 4DZD MET A -18 UNP Q46897 EXPRESSION TAG SEQADV 4DZD GLY A -17 UNP Q46897 EXPRESSION TAG SEQADV 4DZD SER A -16 UNP Q46897 EXPRESSION TAG SEQADV 4DZD SER A -15 UNP Q46897 EXPRESSION TAG SEQADV 4DZD HIS A -14 UNP Q46897 EXPRESSION TAG SEQADV 4DZD HIS A -13 UNP Q46897 EXPRESSION TAG SEQADV 4DZD HIS A -12 UNP Q46897 EXPRESSION TAG SEQADV 4DZD HIS A -11 UNP Q46897 EXPRESSION TAG SEQADV 4DZD HIS A -10 UNP Q46897 EXPRESSION TAG SEQADV 4DZD HIS A -9 UNP Q46897 EXPRESSION TAG SEQADV 4DZD SER A -8 UNP Q46897 EXPRESSION TAG SEQADV 4DZD SER A -7 UNP Q46897 EXPRESSION TAG SEQADV 4DZD GLY A -6 UNP Q46897 EXPRESSION TAG SEQADV 4DZD LEU A -5 UNP Q46897 EXPRESSION TAG SEQADV 4DZD VAL A -4 UNP Q46897 EXPRESSION TAG SEQADV 4DZD PRO A -3 UNP Q46897 EXPRESSION TAG SEQADV 4DZD ARG A -2 UNP Q46897 EXPRESSION TAG SEQADV 4DZD GLY A -1 UNP Q46897 EXPRESSION TAG SEQADV 4DZD SER A 0 UNP Q46897 EXPRESSION TAG SEQRES 1 A 218 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 218 LEU VAL PRO ARG GLY SER MET TYR LEU SER LYS VAL ILE SEQRES 3 A 218 ILE ALA ARG ALA TRP SER ARG ASP LEU TYR GLN LEU HIS SEQRES 4 A 218 GLN GLY LEU TRP HIS LEU PHE PRO ASN ARG PRO ASP ALA SEQRES 5 A 218 ALA ARG ASP PHE LEU PHE HIS VAL GLU LYS ARG ASN THR SEQRES 6 A 218 PRO GLU GLY CYS HIS VAL LEU LEU GLN SER ALA GLN MET SEQRES 7 A 218 PRO VAL SER THR ALA VAL ALA THR VAL ILE LYS THR LYS SEQRES 8 A 218 GLN VAL GLU PHE GLN LEU GLN VAL GLY VAL PRO LEU TYR SEQRES 9 A 218 PHE ARG LEU ARG ALA ASN PRO ILE LYS THR ILE LEU ASP SEQRES 10 A 218 ASN GLN LYS ARG LEU ASP SER LYS GLY ASN ILE LYS ARG SEQRES 11 A 218 CYS ARG VAL PRO LEU ILE LYS GLU ALA GLU GLN ILE ALA SEQRES 12 A 218 TRP LEU GLN ARG LYS LEU GLY ASN ALA ALA ARG VAL GLU SEQRES 13 A 218 ASP VAL HIS PRO ILE SER GLU ARG PRO GLN TYR PHE SER SEQRES 14 A 218 GLY ASP GLY LYS SER GLY LYS ILE GLN THR VAL CYS PHE SEQRES 15 A 218 GLU GLY VAL LEU THR ILE ASN ASP ALA PRO ALA LEU ILE SEQRES 16 A 218 ASP LEU VAL GLN GLN GLY ILE GLY PRO ALA LYS SER MET SEQRES 17 A 218 GLY CYS GLY LEU LEU SER LEU ALA PRO LEU HET GOL A 201 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *143(H2 O) HELIX 1 1 ARG A 10 SER A 13 5 4 HELIX 2 2 ASP A 15 HIS A 25 1 11 HELIX 3 3 LYS A 118 GLY A 131 1 14 HELIX 4 4 ASP A 171 GLY A 182 1 12 HELIX 5 5 ALA A 186 GLY A 190 5 5 SHEET 1 A 4 PHE A 37 THR A 46 0 SHEET 2 A 4 GLY A 49 SER A 56 -1 O GLN A 55 N LEU A 38 SHEET 3 A 4 TYR A 2 ILE A 8 -1 N VAL A 6 O VAL A 52 SHEET 4 A 4 ALA A 66 GLN A 73 -1 O LYS A 72 N LEU A 3 SHEET 1 B 4 ALA A 134 SER A 143 0 SHEET 2 B 4 VAL A 161 ILE A 169 -1 O CYS A 162 N ILE A 142 SHEET 3 B 4 PRO A 83 ALA A 90 -1 N LEU A 88 O PHE A 163 SHEET 4 B 4 LEU A 194 PRO A 198 -1 O ALA A 197 N TYR A 85 SHEET 1 C 2 ILE A 93 LEU A 97 0 SHEET 2 C 2 ARG A 111 PRO A 115 -1 O CYS A 112 N ILE A 96 SHEET 1 D 2 GLN A 147 TYR A 148 0 SHEET 2 D 2 LYS A 157 ILE A 158 -1 O ILE A 158 N GLN A 147 SITE 1 AC1 3 ASP A 36 PHE A 37 LEU A 38 CRYST1 59.900 59.900 128.660 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 0.016694 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007772 0.00000