HEADER HYDROLASE 09-JAN-14 4OCH TITLE APO STRUCTURE OF SMR DOMAIN OF MUTS2 FROM DEINOCOCCUS RADIODURANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE MUTS2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SMR DOMAIN; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS RADIODURANS; SOURCE 3 ORGANISM_TAXID: 243230; SOURCE 4 STRAIN: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / SOURCE 5 NCIMB 9279 / R1 / VKM B-1422; SOURCE 6 GENE: MUTS2, DR_1976; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL(21)DE3 KEYWDS NUCLEASE, MN2+ ION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,Y.ZHAO,Q.XU,Y.J.HUA REVDAT 3 28-FEB-24 4OCH 1 REMARK SEQADV REVDAT 2 20-AUG-14 4OCH 1 JRNL REVDAT 1 25-JUN-14 4OCH 0 JRNL AUTH H.ZHANG,Q.XU,M.LU,X.XU,Y.WANG,L.WANG,Y.ZHAO,Y.HUA JRNL TITL STRUCTURAL AND FUNCTIONAL STUDIES OF MUTS2 FROM DEINOCOCCUS JRNL TITL 2 RADIODURANS. JRNL REF DNA REPAIR V. 21 111 2014 JRNL REFN ISSN 1568-7864 JRNL PMID 24811920 JRNL DOI 10.1016/J.DNAREP.2014.04.012 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 13778 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 681 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 25.6023 - 2.3935 0.99 2707 129 0.1705 0.1837 REMARK 3 2 2.3935 - 1.9000 0.96 2545 139 0.2235 0.2497 REMARK 3 3 1.9000 - 1.6599 0.99 2613 150 0.1763 0.2199 REMARK 3 4 1.6599 - 1.5081 0.99 2642 141 0.1750 0.2189 REMARK 3 5 1.5081 - 1.4001 0.98 2590 122 0.2511 0.3159 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.770 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 : 0.015 674 REMARK 3 ANGLE : 1.776 904 REMARK 3 CHIRALITY : 0.108 101 REMARK 3 PLANARITY : 0.009 120 REMARK 3 DIHEDRAL : 14.821 263 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 4OCH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084318. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.8 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) : 0.97930 REMARK 200 MONOCHROMATOR : SILICON 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13788 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.390 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30MM NACL AND 20MM TRIS-HCL, PH 8.8, REMARK 280 CRYSTAL FORMED SPONTANEOUSLY IN PROTEIN SOLUTION STORED AT 4 REMARK 280 DEGREE, TEMPERATURE 297K 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 23.75500 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 GLY A 677 REMARK 465 HIS A 678 REMARK 465 MET A 679 REMARK 465 GLY A 680 REMARK 465 SER A 681 REMARK 465 ALA A 682 REMARK 465 PRO A 683 REMARK 465 SER A 684 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 801 DBREF 4OCH A 680 766 UNP Q9RSZ3 Q9RSZ3_DEIRA 680 766 SEQADV 4OCH GLY A 677 UNP Q9RSZ3 EXPRESSION TAG SEQADV 4OCH HIS A 678 UNP Q9RSZ3 EXPRESSION TAG SEQADV 4OCH MET A 679 UNP Q9RSZ3 EXPRESSION TAG SEQRES 1 A 90 GLY HIS MET GLY SER ALA PRO SER ARG PHE ASP ASN GLU SEQRES 2 A 90 LEU GLN LEU ARG GLY LEU SER VAL GLU ALA ALA VAL GLU SEQRES 3 A 90 GLU LEU ARG ALA ALA ILE ALA GLU ALA ARG ALA LEU LYS SEQRES 4 A 90 GLU THR PRO LEU ARG VAL VAL HIS GLY LYS GLY MET GLY SEQRES 5 A 90 VAL LEU ARG ARG THR LEU ARG ASP TYR LEU LYS THR ASP SEQRES 6 A 90 LYS ASN VAL GLU SER PHE HIS ASP ALA GLU ALA ASN GLN SEQRES 7 A 90 GLY GLY HIS GLY VAL THR ILE VAL ASN VAL LYS ARG HET GOL A 801 14 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *109(H2 O) HELIX 1 1 SER A 696 LYS A 715 1 20 HELIX 2 2 GLY A 728 LYS A 739 1 12 HELIX 3 3 GLY A 755 HIS A 757 5 3 SHEET 1 A 4 GLU A 689 GLN A 691 0 SHEET 2 A 4 LEU A 719 VAL A 722 1 O ARG A 720 N LEU A 690 SHEET 3 A 4 VAL A 759 VAL A 764 -1 O THR A 760 N VAL A 721 SHEET 4 A 4 VAL A 744 ASP A 749 -1 N HIS A 748 O ILE A 761 CISPEP 1 THR A 717 PRO A 718 0 -4.50 SITE 1 AC1 4 ARG A 732 ASP A 736 HOH A 942 HOH A1008 CRYST1 24.980 47.510 30.810 90.00 99.52 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 0.040032 0.000000 0.006713 0.00000 SCALE2 0.000000 0.021048 0.000000 0.00000 SCALE3 0.000000 0.000000 0.032910 0.00000