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- PDB-2du9: crystal structure of the transcriptional factor from C.glutamicum -

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Basic information

Entry
Database: PDB / ID: 2du9
Titlecrystal structure of the transcriptional factor from C.glutamicum
ComponentsPredicted transcriptional regulators
KeywordsTRANSCRIPTION / winged Helix-turn-Helix
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
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 / 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
Predicted transcriptional regulators
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å
AuthorsGao, Y. / Yao, M. / Tanaka, I.
CitationJournal: Protein Sci. / Year: 2007
Title: The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: A novel homodimer assembling and the implication for effector-binding mode
Authors: Gao, Y. / Yao, M. / Itou, H. / Zhou, Y. / Tanaka, I.
History
DepositionJul 20, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted transcriptional regulators
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5152
Polymers14,3961
Non-polymers1181
Water84747
1
A: Predicted transcriptional regulators
hetero molecules

A: Predicted transcriptional regulators
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0294
Polymers28,7932
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area3060 Å2
ΔGint-46 kcal/mol
Surface area13710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)46.95, 46.95, 152.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a homodimer generated from the monomer by the two fold axis:-y+2, -x+2, -z+1/2

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Components

#1: Protein Predicted transcriptional regulators / Transcription factor / Bacterial regulatory protein / gntR family


Mass: 14396.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: ATCC13032 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8NLJ5
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 12% 2-methyl-2,4 pentanediol, 0.1M Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9790, 0.9793, 0.9000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2005
RadiationMonochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97931
30.91
ReflectionResolution: 2.28→50 Å / Num. all: 8455 / Num. obs: 8392 / % possible obs: 99.3 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 11.7 % / Biso Wilson estimate: 66.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 20.8
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.3 / Num. unique all: 768 / Rsym value: 0.387 / % possible all: 95.6

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.28→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 798 -RANDOM
Rwork0.265 ---
all-8373 --
obs-8143 97.3 %-
Displacement parametersBiso mean: 48.6114 Å2
Baniso -1Baniso -2Baniso -3
1--0.147 Å20 Å20 Å2
2---0.147 Å20 Å2
3---0.293 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.28→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 8 47 945
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0116
X-RAY DIFFRACTIONc_angle_deg1.5692
X-RAY DIFFRACTIONc_dihedral_angle_d20.69578
X-RAY DIFFRACTIONc_improper_angle_d0.93347
LS refinement shellResolution: 2.28→2.36 Å
RfactorNum. reflection% reflection
Rfree0.3817 58 -
Rwork0.3295 --
obs-529 73 %

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