HEADER HYDROLASE 05-OCT-10 3P43 TITLE STRUCTURE AND ACTIVITIES OF ARCHAEAL MEMBERS OF THE LIGD 3' TITLE 2 PHOSPHOESTERASE DNA REPAIR ENZYME SUPERFAMILY COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOSARCINA BARKERI STR. FUSARO; SOURCE 3 ORGANISM_TAXID: 269797; SOURCE 4 STRAIN: FUSARO / DSM 804; SOURCE 5 GENE: MBAR_A2115; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B-SMT3-HIS10 KEYWDS PHOSPHOESTERASE, METALLOENZYME, HYDROLASE, MANGANESE, BETA BARREL EXPDTA X-RAY DIFFRACTION AUTHOR P.SMITH,P.A.NAIR,U.DAS,S.SHUMAN REVDAT 4 06-SEP-23 3P43 1 REMARK SEQADV LINK REVDAT 3 11-MAY-11 3P43 1 JRNL REVDAT 2 02-FEB-11 3P43 1 TITLE REVDAT 1 19-JAN-11 3P43 0 JRNL AUTH P.SMITH,P.A.NAIR,U.DAS,H.ZHU,S.SHUMAN JRNL TITL STRUCTURES AND ACTIVITIES OF ARCHAEAL MEMBERS OF THE LIGD JRNL TITL 2 3'-PHOSPHOESTERASE DNA REPAIR ENZYME SUPERFAMILY. JRNL REF NUCLEIC ACIDS RES. V. 39 3310 2011 JRNL REFN ISSN 0305-1048 JRNL PMID 21208981 JRNL DOI 10.1093/NAR/GKQ1163 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 8458 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 847 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 38.2418 - 3.8149 0.99 1372 153 0.1732 0.2335 REMARK 3 2 3.8149 - 3.0284 0.99 1280 144 0.1886 0.2336 REMARK 3 3 3.0284 - 2.6457 0.97 1258 139 0.2268 0.2765 REMARK 3 4 2.6457 - 2.4038 0.96 1224 136 0.2301 0.3022 REMARK 3 5 2.4038 - 2.2316 0.97 1236 138 0.2323 0.2825 REMARK 3 6 2.2316 - 2.1000 0.97 1241 137 0.2417 0.2883 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 : 0.35 REMARK 3 B_SOL : 37.53 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.97110 REMARK 3 B22 (A**2) : -5.10050 REMARK 3 B33 (A**2) : 9.07170 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 : 0.005 1045 REMARK 3 ANGLE : 0.950 1408 REMARK 3 CHIRALITY : 0.066 144 REMARK 3 PLANARITY : 0.003 180 REMARK 3 DIHEDRAL : 15.322 399 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 3P43 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000061930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 130 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : DOUBLE SILICON(111) CRYSTAL 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8606 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 38.236 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12200 REMARK 200 FOR THE DATA SET : 11.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.46500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.740 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: PDB ENTRY 3N9B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR-DIFFUSION, SITTING-DROP SETUPS REMARK 280 WITH 1:1 MIXTURES OF PROTEIN SOLUTION CONTAINING 0.5 MM MBA AND REMARK 280 2MM MNCL2 AND RESERVOIR SOLUTION CONTAINING PEG 4000 (32%), 0.18 REMARK 280 M MGCL2, 2.5% 1,4-DIOXANE, 0.1 M TRIS-HCL PH 7.5, TEMPERATURE REMARK 280 298K, VAPOR DIFFUSION, SITTING DROP 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 15.18400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.23550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.08300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.23550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.18400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.08300 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 SER A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 TYR A 5 REMARK 465 GLU A 6 REMARK 465 LYS A 7 REMARK 465 LYS A 8 REMARK 465 ARG A 9 REMARK 465 HIS A 10 REMARK 465 PHE A 11 REMARK 465 GLN A 12 REMARK 465 LYS A 13 REMARK 465 THR A 14 REMARK 465 PRO A 15 REMARK 465 GLU A 16 REMARK 465 PRO A 17 REMARK 465 SER A 18 REMARK 465 THR A 19 REMARK 465 THR A 20 REMARK 465 GLY A 21 REMARK 465 VAL A 22 REMARK 465 LYS A 23 REMARK 465 LYS A 24 REMARK 465 SER A 25 REMARK 465 SER A 26 REMARK 465 LYS A 139 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 ASP A 27 N CG OD1 OD2 REMARK 470 GLU A 141 CG CD OE1 OE2 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 LYS A 28 -54.55 -170.91 REMARK 500 ALA A 38 -129.03 -117.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 152 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 36 ND1 REMARK 620 2 HIS A 42 NE2 92.5 REMARK 620 3 ASP A 44 OD2 89.8 102.0 REMARK 620 4 ASP A 44 OD1 141.6 92.0 52.0 REMARK 620 5 PO4 A 201 O3 140.5 101.7 122.0 75.1 REMARK 620 6 PO4 A 201 O1 94.2 143.3 114.0 104.4 53.5 REMARK 620 7 PO4 A 201 O2 90.4 90.9 167.1 127.6 53.2 53.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 152 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 153 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 201 DBREF 3P43 A 1 151 UNP Q46AP6 Q46AP6_METBF 1 151 SEQADV 3P43 SER A 0 UNP Q46AP6 EXPRESSION TAG SEQRES 1 A 152 SER MET LEU GLU GLU TYR GLU LYS LYS ARG HIS PHE GLN SEQRES 2 A 152 LYS THR PRO GLU PRO SER THR THR GLY VAL LYS LYS SER SEQRES 3 A 152 SER ASP LYS PRO ILE PHE VAL VAL GLN ARG HIS ASP ALA SEQRES 4 A 152 ARG LYS LEU HIS TYR ASP PHE ARG LEU GLU MET ASP GLY SEQRES 5 A 152 VAL LEU LYS SER TRP ALA VAL PRO LYS GLU PRO PRO LYS SEQRES 6 A 152 ASP ALA GLY THR ARG ARG LEU ALA ILE GLU THR GLU ASP SEQRES 7 A 152 HIS PRO LEU ALA TYR ALA ASP PHE GLU GLY GLU ILE PRO SEQRES 8 A 152 ALA GLY GLU TYR GLY ALA GLY LYS VAL GLU ILE TRP ASP SEQRES 9 A 152 ARG GLY THR PHE GLU LEU LEU LYS ARG GLU GLU ARG GLU SEQRES 10 A 152 ILE VAL VAL SER LEU GLU GLY LYS GLU LEU LYS GLY ILE SEQRES 11 A 152 TYR VAL LEU ILE ARG THR LYS TYR GLY LYS GLY GLU LYS SEQRES 12 A 152 GLY TRP LEU PHE PHE LYS LYS ALA SER HET MN A 152 1 HET CL A 153 1 HET PO4 A 201 5 HETNAM MN MANGANESE (II) ION HETNAM CL CHLORIDE ION HETNAM PO4 PHOSPHATE ION FORMUL 2 MN MN 2+ FORMUL 3 CL CL 1- FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *92(H2 O) HELIX 1 1 ALA A 81 PHE A 85 5 5 SHEET 1 A 6 HIS A 78 PRO A 79 0 SHEET 2 A 6 VAL A 52 VAL A 58 -1 N LEU A 53 O HIS A 78 SHEET 3 A 6 LEU A 41 MET A 49 -1 N TYR A 43 O VAL A 58 SHEET 4 A 6 ILE A 30 ASP A 37 -1 N GLN A 34 O ASP A 44 SHEET 5 A 6 GLY A 97 GLU A 113 -1 O LYS A 98 N ASP A 37 SHEET 6 A 6 GLY A 87 ILE A 89 -1 N GLY A 87 O VAL A 99 SHEET 1 B 8 HIS A 78 PRO A 79 0 SHEET 2 B 8 VAL A 52 VAL A 58 -1 N LEU A 53 O HIS A 78 SHEET 3 B 8 ARG A 69 GLU A 74 -1 O ILE A 73 N ALA A 57 SHEET 4 B 8 TRP A 144 LYS A 148 -1 O PHE A 146 N ARG A 70 SHEET 5 B 8 LYS A 127 ARG A 134 -1 N ILE A 133 O LEU A 145 SHEET 6 B 8 GLU A 116 GLU A 122 -1 N ILE A 117 O LEU A 132 SHEET 7 B 8 GLY A 97 GLU A 113 -1 N GLU A 108 O SER A 120 SHEET 8 B 8 GLY A 87 ILE A 89 -1 N GLY A 87 O VAL A 99 LINK ND1 HIS A 36 MN MN A 152 1555 1555 2.40 LINK NE2 HIS A 42 MN MN A 152 1555 1555 2.26 LINK OD2 ASP A 44 MN MN A 152 1555 1555 2.23 LINK OD1 ASP A 44 MN MN A 152 1555 1555 2.67 LINK MN MN A 152 O3 PO4 A 201 1555 1555 2.72 LINK MN MN A 152 O1 PO4 A 201 1555 1555 2.74 LINK MN MN A 152 O2 PO4 A 201 1555 1555 2.79 SITE 1 AC1 4 HIS A 36 HIS A 42 ASP A 44 PO4 A 201 SITE 1 AC2 1 LEU A 71 SITE 1 AC3 7 HIS A 36 HIS A 42 ASP A 44 THR A 75 SITE 2 AC3 7 TYR A 94 MN A 152 HOH A 245 CRYST1 30.368 60.166 76.471 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 0.032929 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013077 0.00000