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- PDB-3cag: Crystal structure of the oligomerization domain hexamer of the ar... -

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Basic information

Entry
Database: PDB / ID: 3cag
TitleCrystal structure of the oligomerization domain hexamer of the arginine repressor protein from Mycobacterium tuberculosis in complex with 9 arginines.
ComponentsArginine repressor
KeywordsDNA BINDING PROTEIN / L-Arginine repressor / oligomerization domain / core / alpha/beta topology / TBSGC / Structural Genomics / TB Structural Genomics Consortium / Amino-acid biosynthesis / Arginine biosynthesis / DNA-binding / Transcription / Transcription regulation / PSI-2 / Protein Structure Initiative
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 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 / Arginine repressor / Arginine repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionFeb 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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

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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)50,40015
Polymers48,8236
Non-polymers1,5779
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9470 Å2
ΔGint-18.7 kcal/mol
Surface area16620 Å2
MethodPISA
2
A: Arginine repressor
B: Arginine repressor
C: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4639
Polymers24,4123
Non-polymers1,0516
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-10.2 kcal/mol
Surface area9950 Å2
MethodPISA
3
D: Arginine repressor
E: Arginine repressor
F: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9376
Polymers24,4123
Non-polymers5263
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-11.2 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.745, 75.648, 108.022
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. ACCORDING TO AUTHORS, THE THREE ADDITIONAL LIGANDS (ARG 400) MAY BE RANDOMLY DISTRIBUTED BETWEEN BIOMOLECULES 2 AND 3.

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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 / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG 10000, 0.1M Hepes pH 7.0, 0.2M L-arginine, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.10552 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: 1.10552 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 36125 / Num. obs: 36125 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3141 / Rsym value: 0.422 / % possible all: 84.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-IceIcedata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZFZ

2zfz


Resolution: 1.9→42.26 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.942 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22414 1793 5 %RANDOM
Rwork0.16813 ---
obs0.17083 34288 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.608 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--1.78 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 108 357 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213640
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9984939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84921.765153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52815595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3971551
X-RAY DIFFRACTIONr_chiral_restr0.0990.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022745
X-RAY DIFFRACTIONr_nbd_refined0.2170.21798
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22442
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2349
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.221
X-RAY DIFFRACTIONr_mcbond_it0.961.52455
X-RAY DIFFRACTIONr_mcangle_it1.43223806
X-RAY DIFFRACTIONr_scbond_it2.61631276
X-RAY DIFFRACTIONr_scangle_it4.0574.51133
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 109 -
Rwork0.19 1997 -
obs--76.67 %

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