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- PDB-3ic7: Crystal Structure of Putative Transcriptional Regulator of GntR F... -

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Basic information

Entry
Database: PDB / ID: 3ic7
TitleCrystal Structure of Putative Transcriptional Regulator of GntR Family from Bacteroides thetaiotaomicron
ComponentsPutative transcriptional regulatorTranscriptional regulation
Keywordsstructural genomics / unknown function / helix-turn-helix / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Helix Hairpins - #100 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Helix Hairpins - #100 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / 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
Putative transcriptional regulator
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.819 Å
AuthorsKim, Y. / Sather, A. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Transcriptional Regulator of GntR Family from Bacteroides thetaiotaomicron
Authors: Kim, Y. / Sather, A. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcriptional regulator
B: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)30,0612
Polymers30,0612
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative transcriptional regulator

A: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)30,0612
Polymers30,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area2820 Å2
ΔGint-26 kcal/mol
Surface area15010 Å2
MethodPISA
3
B: Putative transcriptional regulator

B: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)30,0612
Polymers30,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2930 Å2
ΔGint-26 kcal/mol
Surface area14680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.826, 82.826, 85.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsdimer as in the asymmetric unit

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Components

#1: Protein Putative transcriptional regulator / Transcriptional regulation


Mass: 15030.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal 6His-tag with TEV protease cut-site
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_1304 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 magic / References: UniProt: Q8A870
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 45 % MPD, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.504
ReflectionResolution: 2.819→37.24 Å / Num. all: 8473 / Num. obs: 8473 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 78.7 Å2 / Rsym value: 0.096 / Net I/σ(I): 8.3
Reflection shellResolution: 2.82→2.87 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2 / Num. unique all: 412 / Rsym value: 0.717 / % possible all: 96.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
PHENIX(phenix.refine: 1.4_58)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.819→37.24 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.263 394 4.67 %random
Rwork0.236 ---
all0.237 8433 --
obs0.237 8433 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 127.023 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.5293 Å20 Å2-0 Å2
2--21.5293 Å20 Å2
3----43.2561 Å2
Refinement stepCycle: LAST / Resolution: 2.819→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 0 28 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131892
X-RAY DIFFRACTIONf_angle_d1.3872534
X-RAY DIFFRACTIONf_dihedral_angle_d25.159704
X-RAY DIFFRACTIONf_chiral_restr0.084270
X-RAY DIFFRACTIONf_plane_restr0.008324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.8201-3.55020.35182000.30883913411394
3.5502-20.84850.23761930.21684101429495

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