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- PDB-4ob4: Structure of the S. venezulae BldD DNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 4ob4
TitleStructure of the S. venezulae BldD DNA-binding domain
ComponentsPutative DNA-binding protein
KeywordsDNA BINDING PROTEIN / BldD DNA binding domain / helix turn helix
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / nucleotide binding / negative regulation of DNA-templated transcription
Similarity search - Function
DNA-binding protein BldD-like, C-terminal domain / BldD, C-terminal / BldD-like, C-terminal domain superfamily / Helix-turn-helix domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) ...DNA-binding protein BldD-like, C-terminal domain / BldD, C-terminal / BldD-like, C-terminal domain superfamily / Helix-turn-helix domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Authorsschumacher, M.A. / Tschowri, N. / Buttner, M. / Brennan, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development.
Authors: Tschowri, N. / Schumacher, M.A. / Schlimpert, S. / Chinnam, N.B. / Findlay, K.C. / Brennan, R.G. / Buttner, M.J.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative DNA-binding protein
B: Putative DNA-binding protein
C: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)23,6523
Polymers23,6523
Non-polymers00
Water1267
1
A: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)7,8841
Polymers7,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)7,8841
Polymers7,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)7,8841
Polymers7,8841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Putative DNA-binding protein
C: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)15,7682
Polymers15,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-12 kcal/mol
Surface area7400 Å2
MethodPISA
5
B: Putative DNA-binding protein

B: Putative DNA-binding protein


Theoretical massNumber of molelcules
Total (without water)15,7682
Polymers15,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1150 Å2
ΔGint-11 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.970, 79.970, 117.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative DNA-binding protein /


Mass: 7883.973 Da / Num. of mol.: 3 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NCIMB 12804 / NRRL 8165 / MA-4680
Gene: bldD, SAV_6861, SCO1489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7AKQ8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 0.1 M MgCl2, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2013 / Details: mirrors
RadiationMonochromator: si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→69.256 Å / Num. obs: 5897 / % possible obs: 99.9 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2EWT

2ewt


Resolution: 2.8→69.256 Å / SU ML: 0.45 / σ(F): 1.38 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2955 590 10.01 %random
Rwork0.2297 ---
obs0.2363 5897 99.9 %-
all-5309 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.906 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.2029 Å2-0 Å2-0 Å2
2--9.2029 Å20 Å2
3----18.4058 Å2
Refinement stepCycle: LAST / Resolution: 2.8→69.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 0 7 1624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011641
X-RAY DIFFRACTIONf_angle_d1.1652212
X-RAY DIFFRACTIONf_dihedral_angle_d19.095622
X-RAY DIFFRACTIONf_chiral_restr0.066242
X-RAY DIFFRACTIONf_plane_restr0.005290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7999-3.08170.38261430.29831287X-RAY DIFFRACTION100
3.0817-3.52760.3071420.23311281X-RAY DIFFRACTION100
3.5276-4.44430.28651470.21211323X-RAY DIFFRACTION100
4.4443-69.27720.26911580.221416X-RAY DIFFRACTION100

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