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- PDB-3bue: Crystal structure of the C-terminal domain hexamer of ArgR from M... -

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Basic information

Entry
Database: PDB / ID: 3bue
TitleCrystal structure of the C-terminal domain hexamer of ArgR from Mycobacterium tuberculosis
ComponentsArginine repressor ArgR
KeywordsDNA BINDING PROTEIN / L-Arginine repressor protein / oligomerization domain / hexamer / L-arginine binding domain / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Amino-acid biosynthesis / Arginine biosynthesis / DNA-binding / Repressor / Transcription / Transcription regulation / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


regulation of arginine biosynthetic process / : / L-arginine biosynthetic process / arginine binding / protein complex oligomerization / cis-regulatory region sequence-specific DNA binding / transcription regulator complex / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Arginine repressor / Arginine repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / Lu, G.J. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of the C-terminal domain of the arginine repressor protein from Mycobacterium tuberculosis.
Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / Lu, G.J. / James, M.N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression, purification and preliminary X-ray analysis of the C-terminal domain of an arginine repressor protein from Mycobacterium tuberculosis.
Authors: Lu, G.J. / Garen, C.R. / Cherney, M.M. / Cherney, L.T. / Lee, C. / James, M.N.G.
History
DepositionJan 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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: Arginine repressor ArgR
B: Arginine repressor ArgR
C: Arginine repressor ArgR
D: Arginine repressor ArgR
E: Arginine repressor ArgR
F: Arginine repressor ArgR


Theoretical massNumber of molelcules
Total (without water)48,8236
Polymers48,8236
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
MethodPISA
2
A: Arginine repressor ArgR
B: Arginine repressor ArgR
C: Arginine repressor ArgR


Theoretical massNumber of molelcules
Total (without water)24,4123
Polymers24,4123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
MethodPISA
3
D: Arginine repressor ArgR
E: Arginine repressor ArgR
F: Arginine repressor ArgR


Theoretical massNumber of molelcules
Total (without water)24,4123
Polymers24,4123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.219, 57.242, 57.328
Angle α, β, γ (deg.)66.19, 62.21, 82.00
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THAT THE ASYMMETRIC UNIT CONTAINS ONE HEXAMER THAT IS A DIMER OF TRIMERS. EITHER HEXAMER OR TRIMER COULD BE THE BIOLOGICAL UNIT.

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Components

#1: Protein
Arginine repressor ArgR / ArgR


Mass: 8137.206 Da / Num. of mol.: 6 / Fragment: C-terminal domain: Residues 92-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: argR, ahrC, Rv1657, MT1695, MTCY06H11.22 / Plasmid: pGST-1657 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A4Y8, UniProt: P9WPY9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Drops containing 1 microliter protein solution (10 mg/mL) and 0.5 microliter reservoir solution equilibrated against the reservoir solution (20% PEG 10000, 0.1 M HEPES pH 7.5), VAPOR ...Details: Drops containing 1 microliter protein solution (10 mg/mL) and 0.5 microliter reservoir solution equilibrated against the reservoir solution (20% PEG 10000, 0.1 M HEPES pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97848 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 28214 / Num. obs: 28214 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rsym value: 0.061 / Net I/σ(I): 11.77
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.26 / Rsym value: 0.252 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1B4B

1b4b


Resolution: 2.15→44.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.988 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23464 1406 5 %RANDOM
Rwork0.16795 ---
obs0.1712 26786 94.94 %-
all-28194 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.627 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-0.94 Å20.84 Å2
2---0.55 Å20.37 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 0 361 3761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.9994685
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7035463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.76223.182132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88115534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2421536
X-RAY DIFFRACTIONr_chiral_restr0.1110.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022590
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.21525
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22359
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2318
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2321.52391
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97423695
X-RAY DIFFRACTIONr_scbond_it3.41731141
X-RAY DIFFRACTIONr_scangle_it5.494.5990
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 77 -
Rwork0.222 1752 -
obs--82.09 %

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