HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 08-SEP-09 3JRT TITLE STRUCTURE FROM THE MOBILE METAGENOME OF V. PARACHOLERAE: INTEGRON TITLE 2 CASSETTE PROTEIN VPC_CASS2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRON CASSETTE PROTEIN VPC_CASS2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO PARACHOLERAE; SOURCE 3 ORGANISM_TAXID: 650003; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIPL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P15TV LIC KEYWDS INTEGRON CASSETTE PROTEIN, VIBRIO PARACHOLERAE, MOBILE METAGENOME, KEYWDS 2 STRUCTURAL GENOMICS, PSI-2 PROTEIN STRUCTURE INITIATIVE, MIDWEST KEYWDS 3 CENTER FOR STRUCTURAL GENOMICS, MCSG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.J.HARROP,C.DESHPANDE,V.SURESHAN,Y.BOUCHER,X.XU,H.CUI,M.CUFF, AUTHOR 2 A.EDWARDS,A.SAVCHENKO,A.JOACHIMIAK,H.W.STOKES,P.M.G.CURMI, AUTHOR 3 B.C.MABBUTT,MIDWEST CENTER FOR STRUCTURAL GENOMICS (MCSG) REVDAT 2 06-FEB-13 3JRT 1 JRNL VERSN REVDAT 1 22-SEP-09 3JRT 0 JRNL AUTH V.SURESHAN,C.N.DESHPANDE,Y.BOUCHER,J.E.KOENIG,H.W.STOKES, JRNL AUTH 2 S.J.HARROP,P.M.CURMI,B.C.MABBUTT JRNL TITL INTEGRON GENE CASSETTES: A REPOSITORY OF NOVEL PROTEIN FOLDS JRNL TITL 2 WITH DISTINCT INTERACTION SITES. JRNL REF PLOS ONE V. 8 52934 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23349695 JRNL DOI 10.1371/JOURNAL.PONE.0052934 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.4_151) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8782 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.920 REMARK 3 FREE R VALUE TEST SET COUNT : 871 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 27.9920 - 4.1760 1.00 1354 149 0.1720 0.1970 REMARK 3 2 4.1760 - 3.3160 1.00 1326 139 0.1760 0.2550 REMARK 3 3 3.3160 - 2.8980 1.00 1315 147 0.2110 0.2440 REMARK 3 4 2.8980 - 2.6330 1.00 1292 148 0.1980 0.2530 REMARK 3 5 2.6330 - 2.4440 1.00 1313 144 0.2070 0.2610 REMARK 3 6 2.4440 - 2.3000 1.00 1311 144 0.1950 0.2350 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 : 0.30 REMARK 3 B_SOL : 60.88 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.37100 REMARK 3 B22 (A**2) : -5.37100 REMARK 3 B33 (A**2) : 10.74200 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 : 0.008 1369 REMARK 3 ANGLE : 0.968 1847 REMARK 3 CHIRALITY : 0.075 207 REMARK 3 PLANARITY : 0.004 235 REMARK 3 DIHEDRAL : 15.416 511 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: all REMARK 3 ORIGIN FOR THE GROUP (A): 14.2965 29.3796 15.5965 REMARK 3 T TENSOR REMARK 3 T11: -0.1133 T22: 0.2441 REMARK 3 T33: 0.1122 T12: 0.0422 REMARK 3 T13: -0.0720 T23: -0.0851 REMARK 3 L TENSOR REMARK 3 L11: 3.2536 L22: 5.3413 REMARK 3 L33: 4.3897 L12: -0.2580 REMARK 3 L13: -0.7732 L23: 0.8459 REMARK 3 S TENSOR REMARK 3 S11: 0.1190 S12: 0.6913 S13: -0.2238 REMARK 3 S21: 0.0881 S22: -0.1323 S23: 0.5678 REMARK 3 S31: 0.2805 S32: -0.4891 S33: 0.0267 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 3JRT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-09. REMARK 100 THE RCSB ID CODE IS RCSB055078. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-08 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97929 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8801 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.003 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.100 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.50 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 REMARK 200 R SYM FOR SHELL (I) : 0.47300 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX (PHENIX.AUTOSOL) REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M DISODIUM TARTRATE. REMARK 280 IN SITU PROTEOLYSIS WITH CHYMOTRYPSIN, PH 7.3, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 15.55200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.10400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.55200 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.10400 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: 3040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 -1.000000 0.000000 0.000000 42.75500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 74.05383 REMARK 350 BIOMT3 2 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 MSE A -20 REMARK 465 GLY A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 ARG A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 PHE A 75 REMARK 465 GLN A 76 REMARK 465 ALA A 77 REMARK 465 LEU A 78 REMARK 465 LYS A 170 REMARK 465 LEU A 171 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 73 29.63 -74.52 REMARK 500 PRO A 80 -9.45 -42.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC7807 RELATED DB: TARGETDB DBREF 3JRT A -20 171 PDB 3JRT 3JRT -20 171 SEQRES 1 A 192 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 192 ARG GLU ASN LEU TYR PHE GLN GLY VAL LYS MSE SER ASP SEQRES 3 A 192 LYS TRP ILE GLU ILE GLU GLU ILE LEU SER GLY LEU ILE SEQRES 4 A 192 GLY ASP LEU THR ILE ALA VAL THR VAL LEU LYS ASP TYR SEQRES 5 A 192 GLU GLY LYS ALA PHE LEU ARG GLU PRO GLN HIS GLN THR SEQRES 6 A 192 LYS ARG GLN CYS ILE TRP ARG LEU CYS VAL TYR SER ILE SEQRES 7 A 192 VAL ILE ASN CYS ARG LYS TYR VAL GLU LEU ASN GLN LYS SEQRES 8 A 192 TYR GLY LYS GLU PHE GLN ALA LEU ILE PRO GLY HIS ASN SEQRES 9 A 192 HIS ILE ARG GLY VAL TYR ASN ASN GLU ILE ASN LYS ASN SEQRES 10 A 192 THR ALA ILE LYS LYS LEU ARG ASN HIS CYS VAL ALA HIS SEQRES 11 A 192 VAL SER ASP LYS SER LYS TYR LEU LYS PRO ALA GLU VAL SEQRES 12 A 192 GLN GLU GLU ILE ILE LYS MSE PHE ASP GLY ASN PHE ALA SEQRES 13 A 192 ASP GLU PHE LEU ASP TRP ILE CYS PRO ASP ASN ILE SER SEQRES 14 A 192 THR THR ASP LYS SER GLU SER LEU VAL GLY VAL ILE GLU SEQRES 15 A 192 LEU LEU ARG ASP ALA VAL SER ALA LYS LEU MODRES 3JRT MSE A 3 MET SELENOMETHIONINE MODRES 3JRT MSE A 129 MET SELENOMETHIONINE HET MSE A 3 8 HET MSE A 129 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *30(H2 O) HELIX 1 1 ASP A 5 GLY A 33 1 29 HELIX 2 2 LYS A 34 GLN A 41 5 8 HELIX 3 3 HIS A 42 TYR A 71 1 30 HELIX 4 4 ILE A 79 GLY A 81 5 3 HELIX 5 5 HIS A 82 ASN A 96 1 15 HELIX 6 6 ASN A 96 ALA A 108 1 13 HELIX 7 7 LYS A 118 ASP A 131 1 14 HELIX 8 8 ALA A 135 CYS A 143 1 9 HELIX 9 9 ASP A 151 GLU A 154 5 4 HELIX 10 10 SER A 155 SER A 168 1 14 LINK C LYS A 2 N MSE A 3 1555 1555 1.33 LINK C MSE A 3 N SER A 4 1555 1555 1.33 LINK C LYS A 128 N MSE A 129 1555 1555 1.32 LINK C MSE A 129 N PHE A 130 1555 1555 1.33 CRYST1 85.510 85.510 46.656 90.00 90.00 120.00 P 64 6 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 0.011695 0.006752 0.000000 0.00000 SCALE2 0.000000 0.013504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021433 0.00000