PDB Short entry for 1YG2 HEADER TRANSCRIPTION 04-JAN-05 1YG2 TITLE STRUCTURE OF THE VIBRIO CHOLERAE VIRULENCE ACTIVATOR APHA COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENE ACTIVATOR APHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HYPOTHETICAL PROTEIN VC2647; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 STRAIN: N16961 SEROGROUP O1; SOURCE 5 GENE: APHA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: IMPACT-CN FUSION SYSTEM; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PWEL18 KEYWDS VIRULENCE FACTOR; VIBRIO CHOLERAE; WINGED HELIX; TRANSCRIPTION KEYWDS 2 FACTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.S.DE SILVA,G.KOVACIKOVA,W.LIN,R.T.TAYLOR,K.SKORUPSKI,F.J.KULL REVDAT 5 31-JAN-18 1YG2 1 REMARK REVDAT 4 13-JUL-11 1YG2 1 VERSN REVDAT 3 24-FEB-09 1YG2 1 VERSN REVDAT 2 03-MAY-05 1YG2 1 JRNL REVDAT 1 11-JAN-05 1YG2 0 JRNL AUTH R.S.DE SILVA,G.KOVACIKOVA,W.LIN,R.K.TAYLOR,K.SKORUPSKI, JRNL AUTH 2 F.J.KULL JRNL TITL CRYSTAL STRUCTURE OF THE VIRULENCE GENE ACTIVATOR APHA FROM JRNL TITL 2 VIBRIO CHOLERAE REVEALS IT IS A NOVEL MEMBER OF THE WINGED JRNL TITL 3 HELIX TRANSCRIPTION FACTOR SUPERFAMILY JRNL REF J.BIOL.CHEM. V. 280 13779 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15647287 JRNL DOI 10.1074/JBC.M413781200 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2458693.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 11425 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 572 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1752 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 93 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1347 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.29000 REMARK 3 B22 (A**2) : 2.10000 REMARK 3 B33 (A**2) : 6.19000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.36 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.580 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.660 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.620 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.070 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 59.00 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YG2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-03; 01-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; NSLS REMARK 200 BEAMLINE : NULL; X6A REMARK 200 X-RAY GENERATOR MODEL : RIGAKU; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 0.9800 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE; ADSC REMARK 200 QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11425 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 42.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 <I/SIGMA(I)> 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) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.30000 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, MAGENESIUM SULPHATE, PH 6.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 100K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 29.82000 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 29.82000 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 38.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.32500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 38.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.32500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.82000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 38.75000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.32500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 29.82000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 38.75000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.32500 REMARK 290 SMTRY3 8 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 300 REMARK: BIOLOGICAL UNIT IS A DIMER 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 94.65000 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 MET A 1 REMARK 465 PRO A 59 REMARK 465 GLN A 60 REMARK 465 GLU A 61 REMARK 465 GLY A 62 REMARK 465 LYS A 63 REMARK 465 PRO A 64 REMARK 465 ASP A 65 REMARK 465 ARG A 66 REMARK 465 LYS A 67 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 TYR A 19 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 23 CG CD CE NZ 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 ALA A 27 -129.11 -120.74 REMARK 500 LEU A 57 -72.84 -107.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 1YG2 A 1 179 UNP Q9X399 Q9X399_VIBCH 1 179 SEQRES 1 A 179 MET SER LEU PRO HIS VAL ILE LEU THR VAL LEU SER THR SEQRES 2 A 179 ARG ASP ALA THR GLY TYR ASP ILE THR LYS GLU PHE SER SEQRES 3 A 179 ALA SER ILE GLY TYR PHE TRP LYS ALA SER HIS GLN GLN SEQRES 4 A 179 VAL TYR ARG GLU LEU ASN LYS MET GLY GLU GLN GLY LEU SEQRES 5 A 179 VAL THR CYS VAL LEU GLU PRO GLN GLU GLY LYS PRO ASP SEQRES 6 A 179 ARG LYS VAL TYR SER ILE THR GLN ALA GLY ARG SER ALA SEQRES 7 A 179 LEU GLY GLU TRP PHE ASP GLN PRO THR ALA HIS PRO THR SEQRES 8 A 179 VAL ARG ASP GLU PHE SER ALA LYS LEU MET ALA CYS SER SEQRES 9 A 179 VAL GLN SER ALA GLU PRO TYR ARG LEU GLN LEU ALA GLU SEQRES 10 A 179 LEU VAL GLU GLU SER ARG LYS LEU VAL ALA HIS TYR GLN SEQRES 11 A 179 GLU ILE GLU ALA ALA TYR TYR ALA ASN PRO ALA VAL LEU SEQRES 12 A 179 ASP LYS GLN GLN ARG LEU GLU ARG LEU THR LEU ARG ARG SEQRES 13 A 179 ASN LEU LEU VAL ARG GLN ALA TRP ILE GLN TRP ALA ASP SEQRES 14 A 179 GLU VAL LEU ALA GLU LEU ASN ALA MET ALA FORMUL 2 HOH *89(H2 O) HELIX 1 1 SER A 2 ARG A 14 1 13 HELIX 2 2 THR A 17 SER A 26 1 10 HELIX 3 3 ALA A 27 PHE A 32 5 6 HELIX 4 4 SER A 36 GLN A 50 1 15 HELIX 5 5 THR A 72 GLN A 85 1 14 HELIX 6 6 ASP A 94 ALA A 102 1 9 HELIX 7 7 CYS A 103 VAL A 105 5 3 HELIX 8 8 SER A 107 TYR A 137 1 31 HELIX 9 9 ASN A 139 LEU A 143 5 5 HELIX 10 10 ASP A 144 MET A 178 1 35 SHEET 1 A 2 VAL A 53 CYS A 55 0 SHEET 2 A 2 TYR A 69 ILE A 71 -1 O SER A 70 N THR A 54 CRYST1 77.500 94.650 59.640 90.00 90.00 90.00 C 2 2 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 0.012903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010565 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016767 0.00000