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- PDB-2hqb: Crystal Structure of a Transcriptional Activator of comK gene fro... -

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Basic information

Entry
Database: PDB / ID: 2hqb
TitleCrystal Structure of a Transcriptional Activator of comK gene from Bacillus halodurans
ComponentsTranscriptional activator of comK gene
KeywordsTRANSCRIPTION / Berkeley Structure Genomics Center Target 1957B / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


: / ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional activator of comK protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsXu, Q.S. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of a transcriptional activator of comK gene from Bacillus halodurans.
Authors: Xu, Q.S. / Ankoudinova, I. / Lou, Y. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator of comK gene


Theoretical massNumber of molelcules
Total (without water)32,8991
Polymers32,8991
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.117, 90.117, 242.826
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Transcriptional activator of comK gene


Mass: 32899.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: med / Plasmid: pLIC.B3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9K8W3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.32 Å3/Da / Density % sol: 71.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 2.2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97964 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2005 / Details: mirrors
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 2.7→42.2 Å / Num. all: 15980 / Num. obs: 15980 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 19.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3 / Num. unique all: 1540 / Rsym value: 0.358 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→42.24 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2564103.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1571 9.8 %RANDOM
Rwork0.237 ---
all0.241 15976 --
obs0.237 15976 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.0148 Å2 / ksol: 0.355405 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.87 Å216.3 Å20 Å2
2--10.87 Å20 Å2
3----21.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.7→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 0 12 2229
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it3.662
X-RAY DIFFRACTIONc_mcangle_it5.774
X-RAY DIFFRACTIONc_scbond_it8.234
X-RAY DIFFRACTIONc_scangle_it11.146
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.415 143 9.3 %
Rwork0.372 1397 -
obs-1540 95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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