HEADER TRANSCRIPTION 28-DEC-09 3L78 TITLE THE CRYSTAL STRUCTURE OF SMU.1142C FROM STREPTOCOCCUS MUTANS UA159 COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATORY PROTEIN SPX; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-120; COMPND 5 SYNONYM: PUTATIVE TRANSCRIPTIONAL FACTOR SPXA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS MUTANS; SOURCE 3 ORGANISM_TAXID: 210007; SOURCE 4 STRAIN: UA159; SOURCE 5 GENE: SMU.1142C (AMINO ACIDS 1-120); SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS TRANSCRIPTION, TRANSCRIPTIONAL FACTOR, STREPTOCOCCUS MUTANS, KEYWDS 2 DISULFIDE BOND, REDOX-ACTIVE CENTER, TRANSCRIPTION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR X.LIU,T.M.FU,X.-D.SU REVDAT 3 20-NOV-24 3L78 1 REMARK REVDAT 2 01-NOV-23 3L78 1 REMARK REVDAT 1 08-DEC-10 3L78 0 JRNL AUTH X.LIU,T.M.FU,X.-D.SU JRNL TITL THE CRYSTAL STRUCTURE OF SMU.1142C FROM STREPTOCOCCUS MUTANS JRNL TITL 2 UA159 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 9828 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 : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.180 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 36.3251 - 3.6335 1.00 1380 155 0.1858 0.2020 REMARK 3 2 3.6335 - 2.8844 0.99 1300 151 0.1883 0.2634 REMARK 3 3 2.8844 - 2.5199 0.99 1283 140 0.2062 0.2461 REMARK 3 4 2.5199 - 2.2896 0.98 1255 140 0.1719 0.2366 REMARK 3 5 2.2896 - 2.1255 0.96 1235 142 0.1603 0.2018 REMARK 3 6 2.1255 - 2.0002 0.96 1217 133 0.1643 0.2404 REMARK 3 7 2.0002 - 1.9000 0.93 1158 139 0.1923 0.2877 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 : 57.45 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.06800 REMARK 3 B22 (A**2) : 8.91200 REMARK 3 B33 (A**2) : -7.84400 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 : 0.004 972 REMARK 3 ANGLE : 0.813 1317 REMARK 3 CHIRALITY : 0.056 155 REMARK 3 PLANARITY : 0.003 171 REMARK 3 DIHEDRAL : 15.555 375 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): -1.8340 -5.7840 3.7930 REMARK 3 T TENSOR REMARK 3 T11: 0.1273 T22: 0.1431 REMARK 3 T33: 0.1188 T12: -0.0021 REMARK 3 T13: -0.0081 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.6367 L22: 0.6599 REMARK 3 L33: -0.0203 L12: -0.3010 REMARK 3 L13: 0.1980 L23: 0.0859 REMARK 3 S TENSOR REMARK 3 S11: -0.0925 S12: -0.0775 S13: -0.0351 REMARK 3 S21: 0.0590 S22: 0.0459 S23: 0.0214 REMARK 3 S31: -0.0929 S32: 0.0332 S33: 0.0306 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 3L78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9865 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.30 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : 0.31900 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1Z3E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.85 NANO3, 0.1M NACAD PH 6.5, 15% PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K, PH 8.5 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 22.78250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.19800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.73650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 28.19800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.78250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.73650 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 TYR A 118 REMARK 465 ARG A 119 REMARK 465 LYS A 120 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 LYS A 62 CE NZ REMARK 470 GLN A 65 CG CD OE1 NE2 REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 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 A 58 76.51 -69.54 REMARK 500 REMARK 500 REMARK: NULL DBREF 3L78 A 1 120 UNP Q8DU17 SPX_STRMU 1 120 SEQRES 1 A 120 MET VAL THR LEU PHE LEU SER PRO SER CYS THR SER CYS SEQRES 2 A 120 ARG LYS ALA ARG ALA TRP LEU ASN ARG HIS ASP VAL VAL SEQRES 3 A 120 PHE GLN GLU HIS ASN ILE MET THR SER PRO LEU SER ARG SEQRES 4 A 120 ASP GLU LEU LEU LYS ILE LEU SER TYR THR GLU ASN GLY SEQRES 5 A 120 THR GLU ASP ILE ILE SER THR ARG SER LYS VAL PHE GLN SEQRES 6 A 120 LYS LEU ASP ILE ASP VAL ASP GLU LEU SER VAL SER GLU SEQRES 7 A 120 LEU ILE ASN LEU ILE SER LYS ASN PRO SER LEU LEU ARG SEQRES 8 A 120 ARG PRO ILE ILE MET ASP ASN LYS ARG MET GLN ILE GLY SEQRES 9 A 120 PHE ASN GLU ASP GLU ILE ARG ALA PHE LEU PRO ARG ASP SEQRES 10 A 120 TYR ARG LYS FORMUL 2 HOH *46(H2 O) HELIX 1 1 CYS A 10 HIS A 23 1 14 HELIX 2 2 SER A 38 THR A 49 1 12 HELIX 3 3 GLY A 52 ILE A 57 1 6 HELIX 4 4 SER A 61 LEU A 67 1 7 HELIX 5 5 ASP A 70 LEU A 74 5 5 HELIX 6 6 SER A 75 ASN A 86 1 12 HELIX 7 7 PRO A 87 LEU A 90 5 4 HELIX 8 8 ASP A 108 LEU A 114 5 7 SHEET 1 A 4 PHE A 27 ASN A 31 0 SHEET 2 A 4 VAL A 2 LEU A 6 1 N LEU A 4 O HIS A 30 SHEET 3 A 4 ILE A 94 MET A 96 -1 O ILE A 94 N PHE A 5 SHEET 4 A 4 MET A 101 ILE A 103 -1 O GLN A 102 N ILE A 95 SSBOND 1 CYS A 10 CYS A 13 1555 1555 2.04 CISPEP 1 ARG A 92 PRO A 93 0 -5.66 CRYST1 45.565 47.473 56.396 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 0.021947 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017732 0.00000