HEADER TRANSCRIPTION 31-OCT-08 3F3X
TITLE CRYSTAL STRUCTURE OF THE TRANSCRIPTIONAL REGULATOR BLDR FROM
TITLE 2 SULFOLOBUS SOLFATARICUS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR, MARR FAMILY, PUTATIVE;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS;
SOURCE 3 ORGANISM_TAXID: 2287;
SOURCE 4 GENE: SSO1352;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRC
KEYWDS DNA BINDING PROTEIN, TRANSCRIPTIONAL REGULATOR, DNA-BINDING,
KEYWDS 2 TRANSCRIPTION, TRANSCRIPTION REGULATION
EXPDTA X-RAY DIFFRACTION
AUTHOR A.DI FIORE,G.DE SIMONE
REVDAT 3 27-DEC-23 3F3X 1 REMARK
REVDAT 2 25-OCT-17 3F3X 1 REMARK
REVDAT 1 05-MAY-09 3F3X 0
JRNL AUTH A.DI FIORE,G.FIORENTINO,R.M.VITALE,R.RONCA,P.AMODEO,
JRNL AUTH 2 C.PEDONE,S.BARTOLUCCI,G.DE SIMONE
JRNL TITL STRUCTURAL ANALYSIS OF BLDR FROM SULFOLOBUS SOLFATARICUS
JRNL TITL 2 PROVIDES INSIGHTS INTO THE MOLECULAR BASIS OF
JRNL TITL 3 TRANSCRIPTIONAL ACTIVATION IN ARCHAEA BY MARR FAMILY
JRNL TITL 4 PROTEINS.
JRNL REF J.MOL.BIOL. V. 388 559 2009
JRNL REFN ISSN 0022-2836
JRNL PMID 19298823
JRNL DOI 10.1016/J.JMB.2009.03.030
REMARK 2
REMARK 2 RESOLUTION. 1.90 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) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1
REMARK 3 NUMBER OF REFLECTIONS : 13049
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.201
REMARK 3 FREE R VALUE : 0.230
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 670
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1122
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 5
REMARK 3 SOLVENT ATOMS : 108
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) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.008
REMARK 3 BOND ANGLES (DEGREES) : 1.200
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
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 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3F3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-NOV-08.
REMARK 100 THE DEPOSITION ID IS D_1000050115.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 20-MAY-06; 01-NOV-06
REMARK 200 TEMPERATURE (KELVIN) : 100; 100
REMARK 200 PH : 7.8
REMARK 200 NUMBER OF CRYSTALS USED : 2
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y; Y
REMARK 200 RADIATION SOURCE : ELETTRA; ESRF
REMARK 200 BEAMLINE : 5.2R; ID29
REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.2; 0.9792, 0.9794, 0.9757
REMARK 200 MONOCHROMATOR : NULL; NULL
REMARK 200 OPTICS : NULL; NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD; CCD
REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM; ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13332
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 8.400
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.06300
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.7000
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) : 1.97
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.34100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.200
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SOLVE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.33
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULPHATE, 0.1M HEPES, PH
REMARK 280 7.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
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 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-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 21.62000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.05500
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.05500
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.43000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.05500
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.05500
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 10.81000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.05500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.05500
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.43000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.05500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.05500
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 10.81000
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 21.62000
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: 6060 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14290 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 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 0.000000 -1.000000 0.000000 86.11000
REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 86.11000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 21.62000
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 SER A 141
REMARK 465 SER A 142
REMARK 465 LYS A 143
REMARK 465 ASP A 144
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 GLY A 140 CA C O
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 ASP A 88 80.06 -176.19
REMARK 500 ARG A 89 3.23 -55.79
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 SO4 A 201
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2GXG RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF EMRR HOMOLOG FROM HYPERTHERMOPHILIC ARCHAEA
REMARK 900 SULFOLOBUS TOKODAII STRAIN7
DBREF 3F3X A 1 144 UNP Q97YG9 Q97YG9_SULSO 1 144
SEQRES 1 A 144 MET GLN LYS ILE ASP GLU LYS LEU GLN LEU MET ASN THR
SEQRES 2 A 144 ILE ALA LYS ILE TYR ARG GLY SER ILE LYS GLU PHE ASN
SEQRES 3 A 144 ASN ARG LEU GLY LYS LEU MET ASN LEU SER TYR LEU ASP
SEQRES 4 A 144 PHE SER ILE LEU LYS ALA THR SER GLU GLU PRO ARG SER
SEQRES 5 A 144 MET VAL TYR LEU ALA ASN ARG TYR PHE VAL THR GLN SER
SEQRES 6 A 144 ALA ILE THR ALA ALA VAL ASP LYS LEU GLU ALA LYS GLY
SEQRES 7 A 144 LEU VAL ARG ARG ILE ARG ASP SER LYS ASP ARG ARG ILE
SEQRES 8 A 144 VAL ILE VAL GLU ILE THR PRO LYS GLY ARG GLN VAL LEU
SEQRES 9 A 144 LEU GLU ALA ASN GLU VAL LEU ARG ASN LEU VAL ASN GLU
SEQRES 10 A 144 MET LEU SER ASP VAL GLU ASN VAL GLU GLU LEU LEU GLU
SEQRES 11 A 144 GLY LEU ASN LYS ILE LEU SER ARG ILE GLY SER SER LYS
SEQRES 12 A 144 ASP
HET SO4 A 201 5
HETNAM SO4 SULFATE ION
FORMUL 2 SO4 O4 S 2-
FORMUL 3 HOH *108(H2 O)
HELIX 1 1 GLN A 2 ASN A 34 1 33
HELIX 2 2 SER A 36 GLU A 49 1 14
HELIX 3 3 MET A 53 PHE A 61 1 9
HELIX 4 4 THR A 63 LYS A 77 1 15
HELIX 5 5 THR A 97 LEU A 119 1 23
HELIX 6 6 ASN A 124 ILE A 139 1 16
SHEET 1 A 3 ARG A 51 SER A 52 0
SHEET 2 A 3 ASP A 88 ILE A 96 -1 O VAL A 94 N ARG A 51
SHEET 3 A 3 VAL A 80 ASP A 85 -1 N ILE A 83 O ILE A 93
SITE 1 AC1 9 GLN A 9 ASN A 12 LYS A 16 LYS A 44
SITE 2 AC1 9 ARG A 59 TYR A 60 HOH A 305 HOH A 308
SITE 3 AC1 9 HOH A 310
CRYST1 86.110 86.110 43.240 90.00 90.00 90.00 P 43 21 2 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 0.011613 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011613 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023127 0.00000
(ATOM LINES ARE NOT SHOWN.)
END