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- PDB-2fbk: The Crystal Structure of HucR from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 2fbk
TitleThe Crystal Structure of HucR from Deinococcus radiodurans
Componentstranscriptional regulator, MarR family
KeywordsTRANSCRIPTION / winged-helix-turn-helix
Function / homology
Function and homology information


response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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
Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsBordelon, T. / Wilkinson, S.P. / Grove, A. / Newcomer, M.E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of the Transcriptional Regulator HucR from Deinococcus radiodurans Reveals a Repressor Preconfigured for DNA Binding.
Authors: Bordelon, T. / Wilkinson, S.P. / Grove, A. / Newcomer, M.E.
History
DepositionDec 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: transcriptional regulator, MarR family
B: transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5464
Polymers39,4752
Non-polymers712
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-72 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.991, 44.991, 284.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein transcriptional regulator, MarR family


Mass: 19737.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Plasmid: pET5-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9RV71
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG 3350, 500 mM MgCl2, 100 mM Bis-Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1981
21
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.380, 0.9795, 0.9798, 0.9500
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1multilayerMADMx-ray1
2multilayerSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.381
20.97951
30.97981
40.951
ReflectionResolution: 2.3→50 Å / Num. all: 14303 / Num. obs: 14303 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.075 / Net I/σ(I): 12.1
Reflection shellResolution: 2.3→2.44 Å / % possible all: 90

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→38.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 180381.531 / 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
Rfree0.289 1371 9.8 %RANDOM
Rwork0.239 ---
all-14014 --
obs-14014 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.645 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 52.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.14 Å2-0.96 Å20 Å2
2--6.14 Å20 Å2
3----12.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 2 187 2575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 239 11.1 %
Rwork0.32 1923 -
obs-2162 90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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