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- PDB-2zfz: Crystal structure of the C-terminal domain hexamer of ArgR from M... -

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Basic information

Entry
Database: PDB / ID: 2zfz
TitleCrystal structure of the C-terminal domain hexamer of ArgR from Mycobacterium tuberculosis in complex with arginine
ComponentsArginine repressor
KeywordsDNA BINDING PROTEIN / L-ARGININE REPRESSOR / CORE / OLIGOMERIZATION DOMAIN / ALPHA/BETA TOPOLOGY / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Amino-acid biosynthesis / Arginine biosynthesis / DNA-binding / Transcription / Transcription regulation / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


L-arginine biosynthetic process / arginine binding / protein complex oligomerization / 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 / GUANIDINE / Arginine repressor / Arginine repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / Lu, G.J. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: 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.
History
DepositionJan 16, 2008Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Arginine repressor
B: Arginine repressor
C: Arginine repressor
D: Arginine repressor
E: Arginine repressor
F: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,99314
Polymers48,8236
Non-polymers1,1698
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8790 Å2
MethodPISA
2
A: Arginine repressor
B: Arginine repressor
C: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9967
Polymers24,4123
Non-polymers5854
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
MethodPISA
3
D: Arginine repressor
E: Arginine repressor
F: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9967
Polymers24,4123
Non-polymers5854
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.673, 75.947, 107.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE ASYMMETRIC UNIT CONTAINS ONE HEXAMER THAT IS A DIMER OF TRIMERS. EITHER HEXAMER OR TRIMER MIGHT BE THE BIOLOGICAL UNIT.

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Components

#1: Protein
Arginine repressor


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: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 10000, 0.1 M Tris-HCl, 0.1 M Guanidine-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.85→61.9 Å / Num. all: 41086 / Num. obs: 41086 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 17.79
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.03 / Rsym value: 0.8 / % possible all: 99.2

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Processing

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

1b4b


Resolution: 1.85→43.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.248 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22538 2028 4.9 %RANDOM
Rwork0.17686 ---
obs0.17928 38983 99.77 %-
all-39073 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.233 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2--2.05 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.85→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 80 407 3872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.572.0034774
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0725460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69722.714140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56915558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2971542
X-RAY DIFFRACTIONr_chiral_restr0.0980.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022648
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21703
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22412
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9461.52416
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37223732
X-RAY DIFFRACTIONr_scbond_it2.61531189
X-RAY DIFFRACTIONr_scangle_it4.0974.51042
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 149 -
Rwork0.263 2795 -
obs--98.4 %

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