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- PDB-3pqk: Crystal Structure of the transcriptional repressor BigR from Xyle... -

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Basic information

Entry
Database: PDB / ID: 3pqk
TitleCrystal Structure of the transcriptional repressor BigR from Xylella fastidiosa
ComponentsBiofilm growth-associated repressor
KeywordsTRANSCRIPTION / helix-turn-helix motif / winged-helix fold / transcriptional repressor / DNA binding
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription
Similarity search - Function
Helix-turn-helix domain / ArsR-type HTH domain profile. / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biofilm growth-associated repressor
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.09 Å
AuthorsBenedetti, C.E. / Guimaraes, B.G.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Plant Pathogenic Bacteria Utilize Biofilm Growth-associated Repressor (BigR), a Novel Winged-helix Redox Switch, to Control Hydrogen Sulfide Detoxification under Hypoxia.
Authors: Guimaraes, B.G. / Barbosa, R.L. / Soprano, A.S. / Campos, B.M. / de Souza, T.A. / Tonoli, C.C. / Leme, A.F. / Murakami, M.T. / Benedetti, C.E.
History
DepositionNov 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biofilm growth-associated repressor
B: Biofilm growth-associated repressor
C: Biofilm growth-associated repressor
D: Biofilm growth-associated repressor
E: Biofilm growth-associated repressor
F: Biofilm growth-associated repressor


Theoretical massNumber of molelcules
Total (without water)69,3976
Polymers69,3976
Non-polymers00
Water2,396133
1
A: Biofilm growth-associated repressor
B: Biofilm growth-associated repressor


Theoretical massNumber of molelcules
Total (without water)23,1322
Polymers23,1322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-28 kcal/mol
Surface area10870 Å2
MethodPISA
2
C: Biofilm growth-associated repressor
D: Biofilm growth-associated repressor


Theoretical massNumber of molelcules
Total (without water)23,1322
Polymers23,1322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-29 kcal/mol
Surface area11000 Å2
MethodPISA
3
E: Biofilm growth-associated repressor
F: Biofilm growth-associated repressor


Theoretical massNumber of molelcules
Total (without water)23,1322
Polymers23,1322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-29 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.230, 34.230, 140.830
Angle α, β, γ (deg.)90.03, 90.00, 120.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Biofilm growth-associated repressor


Mass: 11566.209 Da / Num. of mol.: 6 / Fragment: UNP residues 13-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Gene: bigR, XF_0767 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PFB1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.76 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.97954 / Wavelength: 0.97954, 0.9795, 0.9797, 0.9282
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 20, 2006
RadiationMonochromator: Si 111 DCM / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.97951
30.97971
40.92821
ReflectionResolution: 2.09→45 Å / Num. all: 32752 / Num. obs: 30801 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 30.48 Å2 / Net I/σ(I): 11.33
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.8 / % possible all: 92.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
BUSTER2.9.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.09→18.49 Å / SU R Cruickshank DPI: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 1539 5 %RANDOM
Rwork0.2095 ---
obs0.2111 30782 93.95 %-
all-30782 --
Displacement parametersBiso mean: 37.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.282 Å
Refinement stepCycle: LAST / Resolution: 2.09→18.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 0 0 133 4736
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0146512
X-RAY DIFFRACTIONt_angle_deg1.0362902
X-RAY DIFFRACTIONt_dihedral_angle_d16802
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1322
X-RAY DIFFRACTIONt_gen_planes6695
X-RAY DIFFRACTIONt_it465120
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion18.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion6405
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact55804
LS refinement shellResolution: 2.09→2.16 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2768 145 4.98 %
Rwork0.2461 2769 -
all0.2476 2914 -
obs--93.95 %

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