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- PDB-3aai: X-ray crystal structure of CsoR from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 3aai
TitleX-ray crystal structure of CsoR from Thermus thermophilus HB8
ComponentsCopper homeostasis operon regulatory protein
KeywordsTRANSCRIPTION / All alpha proteins / 4-helix bundle
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / metal ion binding / cytoplasm
Similarity search - Function
Metal-sensitive repressor, helix protomer / Metal-sensitive transcriptional repressor / Metal-sensitive repressor, helix protomer superfamily / Metal-sensitive transcriptional repressor / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Copper-sensing transcriptional repressor CsoR
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsSakamoto, K. / Agari, Y. / Shinkai, A. / Kuramitsu, S.
CitationJournal: Microbiology / Year: 2010
Title: Structural and functional characterization of the transcriptional repressor CsoR from Thermus thermophilus HB8
Authors: Sakamoto, K. / Agari, Y. / Agari, K. / Kuramitsu, S. / Shinkai, A.
History
DepositionNov 17, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper homeostasis operon regulatory protein
B: Copper homeostasis operon regulatory protein
C: Copper homeostasis operon regulatory protein
D: Copper homeostasis operon regulatory protein


Theoretical massNumber of molelcules
Total (without water)44,2734
Polymers44,2734
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-97 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.198, 63.198, 81.033
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Copper homeostasis operon regulatory protein / Transcriptional repressor CsoR


Mass: 11068.237 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1719 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SHL1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5% MPD, 4.25M Na Formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9787, 0.9, 0.9793
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2008
Details: A fixed exit Si double crystal monochromator followed by a two dimensional focusing mirror which is coated in rhodium.
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.91
30.97931
ReflectionResolution: 2.1→50 Å / Num. obs: 21026 / % possible obs: 99.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 55.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 5.5 / Num. unique all: 1098 / % possible all: 99

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→22.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1219833.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2074 9.9 %RANDOM
Rwork0.244 ---
obs0.244 20995 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 91.2801 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å20 Å2
2---2.45 Å20 Å2
3---4.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 2.1→22.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 0 99 2520
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d14.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.751.5
X-RAY DIFFRACTIONc_mcangle_it4.62
X-RAY DIFFRACTIONc_scbond_it6.032
X-RAY DIFFRACTIONc_scangle_it8.152.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 340 9.9 %
Rwork0.25 3087 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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