HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 20-JAN-09 3FXH TITLE CRYSTAL STRUCTURE FROM THE MOBILE METAGENOME OF HALIFAX HARBOUR SEWAGE TITLE 2 OUTFALL: INTEGRON CASSETTE PROTEIN HFX_CASS2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRON GENE CASSETTE PROTEIN HFX_CASS2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 10-114; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCULTURED BACTERIUM; SOURCE 3 ORGANISM_TAXID: 77133; SOURCE 4 GENE: ORF1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIPL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: P15TV LIC KEYWDS INTEGRON CASSETTE PROTEIN, MOBILE METAGENOME, STRUCTURAL GENOMICS, KEYWDS 2 PSI-2, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, MCSG, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR V.SURESHAN,C.DESHPANDE,S.J.HARROP,M.KUDRITSKA,J.E.KOENIG, AUTHOR 2 E.EVDOKIMOVA,C.CHANG,A.M.EDWARDS,A.SAVCHENKO,A.JOACHIMIAK, AUTHOR 3 W.F.DOOLITTLE,H.W.STOKES,P.M.G.CURMI,B.C.MABBUTT,MIDWEST CENTER FOR AUTHOR 4 STRUCTURAL GENOMICS (MCSG) REVDAT 5 06-NOV-24 3FXH 1 SEQADV LINK REVDAT 4 01-NOV-17 3FXH 1 REMARK REVDAT 3 27-MAR-13 3FXH 1 JRNL REVDAT 2 06-FEB-13 3FXH 1 VERSN REVDAT 1 17-FEB-09 3FXH 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. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 9942 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1000 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 26.7900 - 3.5120 0.95 1302 144 0.1850 0.2330 REMARK 3 2 3.5120 - 2.7890 0.97 1302 144 0.1800 0.2400 REMARK 3 3 2.7890 - 2.4370 0.96 1290 151 0.1770 0.2560 REMARK 3 4 2.4370 - 2.2140 0.97 1331 148 0.1800 0.2270 REMARK 3 5 2.2140 - 2.0550 0.97 1293 141 0.1770 0.2220 REMARK 3 6 2.0550 - 1.9340 0.94 1257 146 0.1990 0.2400 REMARK 3 7 1.9340 - 1.8370 0.86 1167 126 0.2300 0.2970 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 : 0.38 REMARK 3 B_SOL : 79.65 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.99300 REMARK 3 B22 (A**2) : -1.29400 REMARK 3 B33 (A**2) : 2.84700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.36600 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 : 0.007 916 REMARK 3 ANGLE : 0.924 1233 REMARK 3 CHIRALITY : 0.064 140 REMARK 3 PLANARITY : 0.004 159 REMARK 3 DIHEDRAL : 15.860 333 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 26.4451 43.0744 8.8555 REMARK 3 T TENSOR REMARK 3 T11: 0.2678 T22: 0.1794 REMARK 3 T33: 0.1567 T12: -0.0047 REMARK 3 T13: -0.0386 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 3.6891 L22: 2.0454 REMARK 3 L33: 5.6240 L12: -0.0069 REMARK 3 L13: 1.1684 L23: -0.1300 REMARK 3 S TENSOR REMARK 3 S11: 0.0296 S12: -0.3332 S13: 0.2585 REMARK 3 S21: 0.3347 S22: -0.2602 S23: -0.1729 REMARK 3 S31: 0.0470 S32: 0.3267 S33: 0.1835 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 3FXH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000051161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97923 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10187 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.837 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.2890 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.87 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.66900 REMARK 200 R SYM FOR SHELL (I) : 0.66900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.018 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRI-LITHIUM CITRATE, 20% PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 20.37200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.41450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 20.37200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.41450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.8 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 40.74400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 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 GLY A 112 REMARK 465 GLU A 113 REMARK 465 VAL A 114 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 ARG A 40 26.32 -146.49 REMARK 500 LYS A 92 -45.56 -134.03 REMARK 500 SER A 93 -60.43 -108.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: APC7779 RELATED DB: TARGETDB DBREF 3FXH A 1 114 UNP B0BHE4 B0BHE4_9BACT 10 123 SEQADV 3FXH MSE A -20 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH GLY A -19 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH SER A -18 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH SER A -17 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH HIS A -16 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH HIS A -15 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH HIS A -14 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH HIS A -13 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH HIS A -12 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH HIS A -11 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH SER A -10 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH SER A -9 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH GLY A -8 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH ARG A -7 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH GLU A -6 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH ASN A -5 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH LEU A -4 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH TYR A -3 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH PHE A -2 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH GLN A -1 UNP B0BHE4 EXPRESSION TAG SEQADV 3FXH GLY A 0 UNP B0BHE4 EXPRESSION TAG SEQRES 1 A 135 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 135 ARG GLU ASN LEU TYR PHE GLN GLY MSE ASN ASN LYS HIS SEQRES 3 A 135 ALA THR SER ALA VAL HIS GLU ILE ILE ARG GLU ILE CYS SEQRES 4 A 135 ARG LEU VAL ASP SER GLY HIS SER MSE THR ARG ASP GLN SEQRES 5 A 135 PHE HIS GLU LEU SER GLU GLN GLU ARG PHE ILE ALA PHE SEQRES 6 A 135 LEU ALA GLU LYS TYR SER SER THR ILE LYS LEU TYR TYR SEQRES 7 A 135 LEU ALA ASP SER SER PRO LEU PHE GLU LYS ASP THR SER SEQRES 8 A 135 SER PHE ILE GLU ASN ALA PHE GLY ARG HIS ALA ASN THR SEQRES 9 A 135 VAL VAL MSE GLU ASP PHE GLY LEU LYS SER ASN ALA LEU SEQRES 10 A 135 LEU LEU ALA ILE ASN ILE CYS LEU ALA ILE LEU ARG GLU SEQRES 11 A 135 ILE ASN GLY GLU VAL MODRES 3FXH MSE A 1 MET SELENOMETHIONINE MODRES 3FXH MSE A 27 MET SELENOMETHIONINE MODRES 3FXH MSE A 86 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 27 8 HET MSE A 86 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *96(H2 O) HELIX 1 1 ASN A 2 SER A 23 1 22 HELIX 2 2 THR A 28 GLN A 38 1 11 HELIX 3 3 ARG A 40 TYR A 49 1 10 HELIX 4 4 GLU A 66 ASN A 82 1 17 HELIX 5 5 VAL A 85 GLY A 90 5 6 HELIX 6 6 ASN A 94 ASN A 111 1 18 LINK C GLY A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N ASN A 2 1555 1555 1.33 LINK C SER A 26 N MSE A 27 1555 1555 1.33 LINK C MSE A 27 N THR A 28 1555 1555 1.33 LINK C VAL A 85 N MSE A 86 1555 1555 1.33 LINK C MSE A 86 N GLU A 87 1555 1555 1.33 CRYST1 40.744 66.829 48.873 90.00 113.52 90.00 C 1 2 1 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 0.024543 0.000000 0.010683 0.00000 SCALE2 0.000000 0.014964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022315 0.00000