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- PDB-3ere: Crystal structure of the arginine repressor protein from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 3ere
TitleCrystal structure of the arginine repressor protein from Mycobacterium tuberculosis in complex with the DNA operator
Components
  • 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DAP*DAP*DCP*DGP*DAP*DTP*DGP*DCP*DAP*DA)-3'
  • 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DCP*DGP*DTP*DTP*DAP*DTP*DGP*DCP*DAP*DA)-3'
  • Arginine repressor
KeywordsDNA BINDING PROTEIN/DNA / Mycobacterium tuberculosis / arginine repressor protein / DNA binding / ArgR-operator complex / Structural Genomics / TB structural genomics / TB Structural Genomics Consortium / TBSGC / Amino-acid biosynthesis / Arginine biosynthesis / DNA-binding / Transcription / Transcription regulation / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


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-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...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-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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Arginine repressor / Arginine repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / Lu, G.J. / James, M.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of the arginine repressor protein in complex with the DNA operator from Mycobacterium tuberculosis.
Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / Lu, G.J. / James, M.N.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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
D: Arginine repressor
A: 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DAP*DAP*DCP*DGP*DAP*DTP*DGP*DCP*DAP*DA)-3'
B: 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DCP*DGP*DTP*DTP*DAP*DTP*DGP*DCP*DAP*DA)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4496
Polymers27,1613
Non-polymers2883
Water1,67593
1
D: Arginine repressor
A: 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DAP*DAP*DCP*DGP*DAP*DTP*DGP*DCP*DAP*DA)-3'
B: 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DCP*DGP*DTP*DTP*DAP*DTP*DGP*DCP*DAP*DA)-3'
hetero molecules

D: Arginine repressor
A: 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DAP*DAP*DCP*DGP*DAP*DTP*DGP*DCP*DAP*DA)-3'
B: 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DCP*DGP*DTP*DTP*DAP*DTP*DGP*DCP*DAP*DA)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,89812
Polymers54,3226
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area7860 Å2
ΔGint-43.7 kcal/mol
Surface area23200 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-15.5 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.128, 94.128, 147.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11D-240-

HOH

DetailsThe biological unit is a trimer generated by the three-fold crystallographic axis or a dimer of trimers that associate by the antiparallel packing dimer interface.

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Components

#1: Protein Arginine repressor


Mass: 17366.635 Da / Num. of mol.: 1
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: DNA chain 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DAP*DAP*DCP*DGP*DAP*DTP*DGP*DCP*DAP*DA)-3'


Mass: 4906.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA strand A
#3: DNA chain 5'-D(*DTP*DTP*DGP*DCP*DAP*DTP*DCP*DGP*DTP*DTP*DAP*DTP*DGP*DCP*DAP*DA)-3'


Mass: 4888.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA strand B
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 1M Ammonium sulfate, 100 mM Bis-tris buffer, 1% PEG 3350, pH 5.5, VAPOR DIFFUSION, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1Ammonium sulfate11
2Bis-trisBis-tris methane11
3PEG 335011
4Ammonium sulfate12
5Bis-trisBis-tris methane12
6PEG 335012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 13952 / Num. obs: 13952 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 76.4 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 36
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1337 / Rsym value: 0.802 / % possible all: 98.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2FZF, 1B4A

2fzf

1b4a


Resolution: 2.5→40 Å / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 700 -random
Rwork0.2274 ---
obs0.2274 13917 99.8 %-
all-13950 --
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1122 650 15 93 1880
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1061
LS refinement shellResolution: 2.5→2.59 Å / Num. reflection Rfree: 40 / Num. reflection obs: 941

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