HEADER UNKNOWN FUNCTION 25-NOV-11 3UT8 TITLE STRUCTURAL VIEW OF A NON PFAM SINGLETON AND CRYSTAL PACKING ANALYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CTHE_2751; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM THERMOCELLUM; SOURCE 3 ORGANISM_TAXID: 203119; SOURCE 4 STRAIN: ATCC 27405 / DSM 1237; SOURCE 5 GENE: CTHE_2751; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS A NON PFAM SINGLETON, CRYSTAL PACKING ANALYSIS, HELICAL FOLD, UNKNOWN KEYWDS 2 FUNCTION, YTOPLASM EXPDTA X-RAY DIFFRACTION AUTHOR C.CHENG,N.SHAW,X.ZHANG,M.ZHANG,W.DING,B.C.WANG,Z.J.LIU REVDAT 2 20-MAR-24 3UT8 1 REMARK SEQADV REVDAT 1 28-MAR-12 3UT8 0 JRNL AUTH C.CHENG,N.SHAW,X.ZHANG,M.ZHANG,W.DING,B.C.WANG,Z.J.LIU JRNL TITL STRUCTURAL VIEW OF A NON PFAM SINGLETON AND CRYSTAL PACKING JRNL TITL 2 ANALYSIS. JRNL REF PLOS ONE V. 7 31673 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22363703 JRNL DOI 10.1371/JOURNAL.PONE.0031673 REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 16720 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 838 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 27.1499 - 3.9358 0.95 2744 119 0.1925 0.1848 REMARK 3 2 3.9358 - 3.1254 0.98 2648 139 0.2171 0.2182 REMARK 3 3 3.1254 - 2.7308 1.00 2677 162 0.2495 0.2565 REMARK 3 4 2.7308 - 2.4813 1.00 2675 134 0.2475 0.2729 REMARK 3 5 2.4813 - 2.3035 1.00 2651 148 0.2528 0.2700 REMARK 3 6 2.3035 - 2.1678 0.94 2487 136 0.2628 0.2171 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 25.09 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.020 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) : 3.16390 REMARK 3 B22 (A**2) : -1.15350 REMARK 3 B33 (A**2) : -6.23990 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 2224 REMARK 3 ANGLE : 1.058 3031 REMARK 3 CHIRALITY : 0.075 351 REMARK 3 PLANARITY : 0.012 369 REMARK 3 DIHEDRAL : 14.009 845 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 3UT8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16720 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.168 REMARK 200 RESOLUTION RANGE LOW (A) : 30.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 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) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 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: NULL REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 25.05250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.45450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.94250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.45450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.05250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.94250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 PRO A 130 REMARK 465 MET B 1 REMARK 465 PRO B 130 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 HIS A 126 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 126 CG ND1 CD2 CE1 NE2 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 SER B 3 82.16 116.64 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER B 106 -23.91 REMARK 500 SER B 106 -23.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD B 132 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UT4 RELATED DB: PDB REMARK 900 RELATED ID: 3UT7 RELATED DB: PDB DBREF 3UT8 A 1 130 UNP A3DJ21 A3DJ21_CLOTH 1 130 DBREF 3UT8 B 1 130 UNP A3DJ21 A3DJ21_CLOTH 1 130 SEQADV 3UT8 TYR A 124 UNP A3DJ21 SER 124 ENGINEERED MUTATION SEQADV 3UT8 TYR A 128 UNP A3DJ21 THR 128 ENGINEERED MUTATION SEQADV 3UT8 TYR A 129 UNP A3DJ21 ILE 129 ENGINEERED MUTATION SEQADV 3UT8 TYR B 124 UNP A3DJ21 SER 124 ENGINEERED MUTATION SEQADV 3UT8 TYR B 128 UNP A3DJ21 THR 128 ENGINEERED MUTATION SEQADV 3UT8 TYR B 129 UNP A3DJ21 ILE 129 ENGINEERED MUTATION SEQRES 1 A 130 MET THR SER LEU ARG ASP LEU ILE PRO LYS HIS LYS PHE SEQRES 2 A 130 ASP ASN SER THR ILE ASP GLN LEU CYS LYS LEU ILE ASP SEQRES 3 A 130 ASN GLU ILE GLU PRO ILE ILE PHE ASP LEU LEU LYS TRP SEQRES 4 A 130 LEU GLN ASP TYR ASN TRP PRO ILE ALA LYS ASP ILE LEU SEQRES 5 A 130 PRO VAL VAL VAL LEU HIS GLN SER ILE ALA MET PRO HIS SEQRES 6 A 130 ILE LEU THR ILE LEU GLN GLY ASN ASP ILE MET TRP LYS SEQRES 7 A 130 TYR TRP VAL ILE LYS LEU MET ILE PRO TYR LEU ILE TYR SEQRES 8 A 130 PRO ASN LYS GLN LEU VAL LYS SER GLU LEU GLU ARG LEU SEQRES 9 A 130 SER SER LEU GLU ILE ILE ASN GLU ASP ILE ARG GLU ILE SEQRES 10 A 130 VAL ASN LEU SER LYS ASP TYR LEU HIS PHE TYR TYR PRO SEQRES 1 B 130 MET THR SER LEU ARG ASP LEU ILE PRO LYS HIS LYS PHE SEQRES 2 B 130 ASP ASN SER THR ILE ASP GLN LEU CYS LYS LEU ILE ASP SEQRES 3 B 130 ASN GLU ILE GLU PRO ILE ILE PHE ASP LEU LEU LYS TRP SEQRES 4 B 130 LEU GLN ASP TYR ASN TRP PRO ILE ALA LYS ASP ILE LEU SEQRES 5 B 130 PRO VAL VAL VAL LEU HIS GLN SER ILE ALA MET PRO HIS SEQRES 6 B 130 ILE LEU THR ILE LEU GLN GLY ASN ASP ILE MET TRP LYS SEQRES 7 B 130 TYR TRP VAL ILE LYS LEU MET ILE PRO TYR LEU ILE TYR SEQRES 8 B 130 PRO ASN LYS GLN LEU VAL LYS SER GLU LEU GLU ARG LEU SEQRES 9 B 130 SER SER LEU GLU ILE ILE ASN GLU ASP ILE ARG GLU ILE SEQRES 10 B 130 VAL ASN LEU SER LYS ASP TYR LEU HIS PHE TYR TYR PRO HET IOD A 131 1 HET IOD A 132 1 HET IOD A 133 1 HET IOD B 131 1 HET IOD B 132 1 HETNAM IOD IODIDE ION FORMUL 3 IOD 5(I 1-) FORMUL 8 HOH *126(H2 O) HELIX 1 1 SER A 3 ILE A 8 5 6 HELIX 2 2 THR A 17 CYS A 22 1 6 HELIX 3 3 ILE A 25 GLU A 30 1 6 HELIX 4 4 ILE A 32 LYS A 38 1 7 HELIX 5 5 TRP A 39 GLN A 41 5 3 HELIX 6 6 ILE A 47 HIS A 58 1 12 HELIX 7 7 GLN A 59 ILE A 61 5 3 HELIX 8 8 ALA A 62 GLY A 72 1 11 HELIX 9 9 ASP A 74 ILE A 86 1 13 HELIX 10 10 PRO A 87 LEU A 89 5 3 HELIX 11 11 ILE A 90 VAL A 97 1 8 HELIX 12 12 VAL A 97 SER A 106 1 10 HELIX 13 13 ASN A 111 TYR A 129 1 19 HELIX 14 14 SER B 3 ILE B 8 5 6 HELIX 15 15 THR B 17 CYS B 22 1 6 HELIX 16 16 ILE B 25 GLU B 30 1 6 HELIX 17 17 ILE B 32 LYS B 38 1 7 HELIX 18 18 TRP B 39 GLN B 41 5 3 HELIX 19 19 TRP B 45 HIS B 58 1 14 HELIX 20 20 GLN B 59 ILE B 61 5 3 HELIX 21 21 ALA B 62 GLY B 72 1 11 HELIX 22 22 ASP B 74 ILE B 86 1 13 HELIX 23 23 PRO B 87 LEU B 89 5 3 HELIX 24 24 ILE B 90 VAL B 97 1 8 HELIX 25 25 VAL B 97 SER B 106 1 10 HELIX 26 26 ASN B 111 TYR B 129 1 19 SITE 1 AC1 1 LEU A 67 SITE 1 AC2 1 HOH A 193 SITE 1 AC3 2 ILE B 75 LYS B 78 CRYST1 50.105 63.885 96.909 90.00 90.00 90.00 P 21 21 21 8 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 0.019958 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015653 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010319 0.00000