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- PDB-2ewt: Crystal structure of the DNA-binding domain of BldD -

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Basic information

Entry
Database: PDB / ID: 2ewt
TitleCrystal structure of the DNA-binding domain of BldD
Componentsputative DNA-binding protein
KeywordsDNA BINDING PROTEIN / the DNA-binding domain of BldD
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
: / DNA-binding protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.81 Å
AuthorsKim, I.K. / Lee, C.J. / Kim, M.K. / Kim, J.M. / Kim, J.H. / Yim, H.S. / Cha, S.S. / Kang, S.O.
Citation
Journal: Mol.Microbiol. / Year: 2006
Title: Crystal structure of the DNA-binding domain of BldD, a central regulator of aerial mycelium formation in Streptomyces coelicolor A3(2)
Authors: Kim, I.K. / Lee, C.J. / Kim, M.K. / Kim, J.M. / Kim, J.H. / Yim, H.S. / Cha, S.S. / Kang, S.O.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray crystallographic analysis of the DNA-binding domain of BldD from Streptomyces coelicolor A3(2)
Authors: Kim, I.K. / Kim, M.K. / Lee, C.J. / Yim, H.S. / Cha, S.S. / Kang, S.O.
History
DepositionNov 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1724
Polymers7,8841
Non-polymers2883
Water2,648147
1
A: putative DNA-binding protein
hetero molecules

A: putative DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3448
Polymers15,7682
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Unit cell
Length a, b, c (Å)77.199, 31.774, 33.644
Angle α, β, γ (deg.)90.00, 105.14, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1, -y, z+3/2

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Components

#1: Protein putative DNA-binding protein / / BldD


Mass: 7883.973 Da / Num. of mol.: 1 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 21219990, UniProt: Q7AKQ8*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25% PEG 4000, 0.1M sodium acetate (pH 4.6), 0.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.97932, 0.97942, 0.98722
DetectorType: MAC Science DIP-2030B / Detector: IMAGE PLATE / Date: Dec 5, 2003
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.979421
30.987221
ReflectionResolution: 1.8→20 Å / Num. all: 7441 / Num. obs: 7031 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.7 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 94.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.81→19.57 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1438212.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 381 5.4 %RANDOM
Rwork0.188 ---
obs0.188 7031 94.5 %-
all-7441 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.3987 Å2 / ksol: 0.351951 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20.04 Å2
2--0.86 Å20 Å2
3----1.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.81→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms551 0 15 147 713
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17.4
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.8→1.91 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.186 999 -
obs--82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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