HEADER HYDROLASE 10-JAN-14 4OD6 TITLE STRUCTURE OF SMR DOMAIN OF MUTS2 FROM DEINOCOCCUS RADIODURANS, MN2+ TITLE 2 SOAKED 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: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NUCLEASE, MN2+, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,Y.ZHAO,Q.XU,Y.J.HUA REVDAT 3 28-FEB-24 4OD6 1 SEQADV REVDAT 2 20-AUG-14 4OD6 1 JRNL REVDAT 1 25-JUN-14 4OD6 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 22694 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 1170 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 26.3159 - 2.3974 0.96 2769 155 0.1701 0.1838 REMARK 3 2 2.3974 - 1.9031 0.95 2651 142 0.1820 0.1926 REMARK 3 3 1.9031 - 1.6626 0.99 2716 132 0.1595 0.1803 REMARK 3 4 1.6626 - 1.5106 1.00 2703 150 0.1503 0.1807 REMARK 3 5 1.5106 - 1.4023 0.99 2705 141 0.1858 0.2445 REMARK 3 6 1.4023 - 1.3196 1.00 2729 132 0.1809 0.2190 REMARK 3 7 1.3196 - 1.2535 0.99 2659 156 0.2565 0.2862 REMARK 3 8 1.2535 - 1.1990 0.98 2592 162 0.2890 0.3600 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.240 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 : 0.019 694 REMARK 3 ANGLE : 1.849 937 REMARK 3 CHIRALITY : 0.093 104 REMARK 3 PLANARITY : 0.011 127 REMARK 3 DIHEDRAL : 13.040 273 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 4OD6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084343. 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 : 22713 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.199 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 (%) : 98.3 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) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30MM NACL AND 20MM TRIS-HCL, SOAKED IN REMARK 280 5MM MNCL2 BEFORE X-RAY DATA COLLECTION, PH 8.8, CRYSTAL FORMED REMARK 280 SPONTANEOUSLY IN PROTEIN SOLUTION STORED AT 4 DEGREE, REMARK 280 TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.56000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.63000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.32000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.63000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.56000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.32000 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: 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 766 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 MET A 727 CG - SD - CE ANGL. DEV. = 10.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 4OD6 A 680 766 UNP Q9RSZ3 Q9RSZ3_DEIRA 680 766 SEQADV 4OD6 GLY A 677 UNP Q9RSZ3 EXPRESSION TAG SEQADV 4OD6 HIS A 678 UNP Q9RSZ3 EXPRESSION TAG SEQADV 4OD6 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 FORMUL 2 HOH *119(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 GLU A 751 HIS A 757 5 7 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 -9.67 CRYST1 31.120 46.640 49.260 90.00 90.00 90.00 P 21 21 21 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 0.032134 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020300 0.00000