HEADER UNKNOWN FUNCTION 05-SEP-11 3TOE TITLE STRUCTURE OF MTH10B COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA-BINDING PROTEIN ALBA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MTH10B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 187420; SOURCE 4 STRAIN: DELTA H; SOURCE 5 GENE: ALBA, MTH_1483; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SAC10B FAMILY, ALPHA/BETA MIXED, HOMODIMER, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR X.M.PAN,N.ZHANG,Y.F.LIU,X.LIU REVDAT 3 01-NOV-23 3TOE 1 REMARK REVDAT 2 01-JAN-20 3TOE 1 JRNL REVDAT 1 25-APR-12 3TOE 0 JRNL AUTH Y.F.LIU,N.ZHANG,X.LIU,X.WANG,Z.X.WANG,Y.CHEN,H.W.YAO,M.GE, JRNL AUTH 2 X.M.PAN JRNL TITL MOLECULAR MECHANISM UNDERLYING THE INTERACTION OF TYPICAL JRNL TITL 2 SAC10B FAMILY PROTEINS WITH DNA. JRNL REF PLOS ONE V. 7 34986 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22511977 JRNL DOI 10.1371/JOURNAL.PONE.0034986 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.74 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 9122 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 431 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 28.7465 - 3.1672 1.00 3056 137 0.2001 0.2479 REMARK 3 2 3.1672 - 2.5144 0.99 2894 143 0.2265 0.3308 REMARK 3 3 2.5144 - 2.1967 0.95 2741 151 0.2630 0.3563 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 : 0.32 REMARK 3 B_SOL : 40.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.39840 REMARK 3 B22 (A**2) : 20.36520 REMARK 3 B33 (A**2) : -13.96690 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 : 0.009 1320 REMARK 3 ANGLE : 1.156 1790 REMARK 3 CHIRALITY : 0.073 226 REMARK 3 PLANARITY : 0.005 232 REMARK 3 DIHEDRAL : 18.181 492 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 12.8099 10.6436 19.5833 REMARK 3 T TENSOR REMARK 3 T11: 0.2601 T22: 0.3272 REMARK 3 T33: 0.2965 T12: -0.0297 REMARK 3 T13: -0.0492 T23: 0.0129 REMARK 3 L TENSOR REMARK 3 L11: 1.1059 L22: 1.3787 REMARK 3 L33: 3.0569 L12: -0.3706 REMARK 3 L13: -1.3563 L23: -0.4381 REMARK 3 S TENSOR REMARK 3 S11: -0.1105 S12: 0.0105 S13: 0.1010 REMARK 3 S21: -0.0157 S22: 0.0762 S23: 0.0211 REMARK 3 S31: 0.2098 S32: -0.1083 S33: -0.0001 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 12.3072 16.8644 37.7365 REMARK 3 T TENSOR REMARK 3 T11: 0.3703 T22: 0.2746 REMARK 3 T33: 0.3618 T12: -0.0189 REMARK 3 T13: 0.0087 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.9966 L22: 1.2078 REMARK 3 L33: 2.5748 L12: 0.0074 REMARK 3 L13: 0.0635 L23: 1.2616 REMARK 3 S TENSOR REMARK 3 S11: 0.0944 S12: -0.3239 S13: -0.0746 REMARK 3 S21: 0.1304 S22: 0.0510 S23: 0.1252 REMARK 3 S31: -0.1225 S32: -0.0687 S33: -0.0001 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 3TOE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067721. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9180 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.197 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 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) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 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: 1H0X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NACL, 1.6M (NH4)2SO4, 0.1M HEPES, REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 26.44800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.12750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.75050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.44800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.12750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.75050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.44800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 38.12750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.75050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.44800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 38.12750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.75050 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: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 SER A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 ASP A 91 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLU B 3 REMARK 465 GLU B 4 REMARK 465 ASP B 91 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE ARG A 89 NE ARG A 89 2555 2.00 REMARK 500 CG ARG A 89 NH2 ARG A 89 2555 2.03 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 6 112.91 37.13 REMARK 500 PHE A 55 -46.93 -135.27 REMARK 500 ASP A 58 -27.54 106.82 REMARK 500 THR B 29 113.98 -23.88 REMARK 500 REMARK 500 REMARK: NULL DBREF 3TOE A 1 91 UNP O27527 ALBA_METTH 1 91 DBREF 3TOE B 1 91 UNP O27527 ALBA_METTH 1 91 SEQRES 1 A 91 MET SER GLU GLU ASN VAL VAL TYR ILE GLY ASN LYS PRO SEQRES 2 A 91 VAL MET ASN TYR VAL LEU ALA VAL VAL THR GLN MET ASN SEQRES 3 A 91 GLY GLY THR SER GLU VAL ILE LEU LYS ALA ARG GLY ILE SEQRES 4 A 91 ALA ILE SER ARG ALA VAL ASP VAL ALA GLU ILE VAL ARG SEQRES 5 A 91 ASN ARG PHE ILE PRO ASP ILE GLN ILE GLU ASN ILE ASP SEQRES 6 A 91 ILE CYS THR GLU GLU ILE ILE GLY ASN GLU GLY THR ALA SEQRES 7 A 91 THR ASN VAL SER ALA ILE GLU ILE GLN LEU ARG LYS ASP SEQRES 1 B 91 MET SER GLU GLU ASN VAL VAL TYR ILE GLY ASN LYS PRO SEQRES 2 B 91 VAL MET ASN TYR VAL LEU ALA VAL VAL THR GLN MET ASN SEQRES 3 B 91 GLY GLY THR SER GLU VAL ILE LEU LYS ALA ARG GLY ILE SEQRES 4 B 91 ALA ILE SER ARG ALA VAL ASP VAL ALA GLU ILE VAL ARG SEQRES 5 B 91 ASN ARG PHE ILE PRO ASP ILE GLN ILE GLU ASN ILE ASP SEQRES 6 B 91 ILE CYS THR GLU GLU ILE ILE GLY ASN GLU GLY THR ALA SEQRES 7 B 91 THR ASN VAL SER ALA ILE GLU ILE GLN LEU ARG LYS ASP HELIX 1 1 PRO A 13 GLY A 27 1 15 HELIX 2 2 ILE A 39 PHE A 55 1 17 HELIX 3 3 PRO B 13 GLY B 27 1 15 HELIX 4 4 ILE B 39 PHE B 55 1 17 SHEET 1 A 4 VAL A 7 TYR A 8 0 SHEET 2 A 4 GLU A 31 ARG A 37 1 O ILE A 33 N VAL A 7 SHEET 3 A 4 ALA A 78 ARG A 89 -1 O LEU A 88 N VAL A 32 SHEET 4 A 4 GLN A 60 ILE A 72 -1 N GLN A 60 O ARG A 89 SHEET 1 B 4 VAL B 6 TYR B 8 0 SHEET 2 B 4 GLU B 31 ARG B 37 1 O LYS B 35 N VAL B 7 SHEET 3 B 4 ALA B 78 ARG B 89 -1 O ILE B 86 N LEU B 34 SHEET 4 B 4 GLN B 60 ILE B 72 -1 N GLU B 69 O VAL B 81 CRYST1 52.896 76.255 87.501 90.00 90.00 90.00 I 2 2 2 16 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 0.018905 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013114 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011428 0.00000