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- PDB-3fhz: Crystal structure of the arginine repressor from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 3fhz
TitleCrystal structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and co-repressor, L-arginine
Components
  • 5'-D(*TP*GP*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*AP*AP*A)-3'
  • 5'-D(*TP*TP*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*AP*CP*A)-3'
  • Arginine repressor
KeywordsDNA BINDING PROTEIN/DNA / Mycobacterium tuberculosis / arginine repressor protein / DNA binding / ArgR-operator ternary complex / Structural Genomics / TB structural genomics / TB Structural Genomics Consortium / TBSGC / Amino-acid biosynthesis / Arginine biosynthesis / DNA-binding / Repressor / 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
ACETATE ION / ARGININE / DNA / DNA (> 10) / Arginine repressor / Arginine repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The structure of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator and Co-repressor, L-arginine.
Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.
History
DepositionDec 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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
A: Arginine repressor
B: Arginine repressor
C: Arginine repressor
D: Arginine repressor
E: Arginine repressor
F: Arginine repressor
G: 5'-D(*TP*GP*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*AP*AP*A)-3'
H: 5'-D(*TP*TP*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*AP*CP*A)-3'
I: 5'-D(*TP*GP*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*AP*AP*A)-3'
J: 5'-D(*TP*TP*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*AP*CP*A)-3'
K: 5'-D(*TP*GP*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*AP*AP*A)-3'
L: 5'-D(*TP*TP*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,78224
Polymers140,99512
Non-polymers1,78712
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36340 Å2
ΔGint-144 kcal/mol
Surface area49550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.286, 152.649, 163.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain G and (resseq 1:20)
211chain K and (resseq 1:20)
311chain I and (resseq 1:20)
112chain H and (resseq 1:20)
212chain L and (resseq 1:20)
312chain J and (resseq 1:20)
113chain D and (resseq 12:170 )
213chain C and (resseq 12:170 )
313chain B and (resseq 12:170 )
114chain A and (resseq 20:170 )
214chain E and (resseq 20:170 )
314chain F and (resseq 20:170 )

NCS ensembles :
ID
1
2
3
4
DetailsThe biological unit is the content of the asymmetric unit: arginine repressor hexamer with bound three copies of the DNA operator and arginine molecules

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Arginine repressor


Mass: 17366.635 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ahrC, argR, MT1695, MTCY06H11.22, Rv1657 / Plasmid: pGST-1657 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P0A4Y8, UniProt: P9WPY9*PLUS

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DNA chain , 2 types, 6 molecules GIKHJL

#2: DNA chain 5'-D(*TP*GP*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*AP*AP*A)-3'


Mass: 6166.030 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: 20 oligonucleotide DNA segment 1
#3: DNA chain 5'-D(*TP*TP*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*AP*CP*A)-3'


Mass: 6098.964 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: 20 oligonucleotide DNA segment 2

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Non-polymers , 4 types, 85 molecules

#4: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 100mM Bis-tris, 0.2M KF, 15% Glycerol, 10mM Arginine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 335011
2Bis-trisBis-tris methane11
3Potassium fluoride11
4Glycerol11
5Arginine11
6PEG 335012
7Bis-trisBis-tris methane12
8Potassium fluoride12
9Glycerol12
10Arginine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.27→50 Å / Num. obs: 24627 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 96.4 Å2 / Rsym value: 0.095 / Net I/σ(I): 11.3
Reflection shellResolution: 3.27→3.42 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.57 / Num. unique all: 2445 / Rsym value: 0.563 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2FZF, 3ERE

2fzf

3ere


Resolution: 3.27→44.339 Å / SU ML: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2757 1246 5.06 %random
Rwork0.2306 ---
obs0.2329 24605 97.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.592 Å2 / ksol: 0.314 e/Å3
Refinement stepCycle: LAST / Resolution: 3.27→44.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6841 2442 98 73 9454
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg0.864
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11G410X-RAY DIFFRACTIONPOSITIONAL
12K410X-RAY DIFFRACTIONPOSITIONAL0.007
13I410X-RAY DIFFRACTIONPOSITIONAL0.008
21H404X-RAY DIFFRACTIONPOSITIONAL
22L404X-RAY DIFFRACTIONPOSITIONAL0.008
23J404X-RAY DIFFRACTIONPOSITIONAL0.009
31D1145X-RAY DIFFRACTIONPOSITIONAL
32C1145X-RAY DIFFRACTIONPOSITIONAL0.084
33B1145X-RAY DIFFRACTIONPOSITIONAL0.053
41A1088X-RAY DIFFRACTIONPOSITIONAL
42E1088X-RAY DIFFRACTIONPOSITIONAL0.085
43F1088X-RAY DIFFRACTIONPOSITIONAL0.054
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.27-3.40080.34381280.3154231288
3.4008-3.55560.36151360.2982260099
3.5556-3.74290.36311460.2749260599
3.7429-3.97730.31551300.24152618100
3.9773-4.28410.30091490.2231260899
4.2841-4.71480.25551390.1909261199
4.7148-5.39610.23971390.1983263799
5.3961-6.79450.26031430.2222265298
6.7945-44.34350.21271360.2005271695

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