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- PDB-3laj: The Structure of the Intermediate Complex of the Arginine Repress... -

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Basic information

Entry
Database: PDB / ID: 3laj
TitleThe Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound to its DNA Operator and L-arginine.
Components
  • 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
  • 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
  • Arginine repressor
KeywordsTRANSCRIPTION REGULATOR / Mycobacterium tuberculosis / arginine repressor / DNA binding / ArgR-DNA complex / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB / Amino-acid biosynthesis / Arginine biosynthesis / Cytoplasm / DNA-binding / Repressor / Transcription
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
ARGININE / DNA / DNA (> 10) / Arginine repressor / Arginine repressor
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsCherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.G. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression.
Authors: Cherney, L.T. / Cherney, M.M. / Garen, C.R. / James, M.N.
History
DepositionJan 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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
A: Arginine repressor
B: Arginine repressor
C: Arginine repressor
D: Arginine repressor
E: Arginine repressor
F: Arginine repressor
G: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
H: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
I: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
J: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
K: 5'-D(*TP*TP*GP*CP*AP*TP*AP*AP*CP*GP*AP*TP*GP*CP*AP*A)-3'
L: 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,63418
Polymers133,58312
Non-polymers1,0516
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28580 Å2
ΔGint-99 kcal/mol
Surface area46190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.686, 106.788, 119.080
Angle α, β, γ (deg.)90.00, 121.75, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
13
23
33
14
24
34
15
25
35

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain F and (resseq 17:170 )
211chain E and (resseq 17:170 )
311chain D and (resseq 17:170 )
112chain B and (resseq 90:170 )
212chain A and (resseq 90:170 )
312chain C and (resseq 90:170 )
113chain A and (resseq 15:82 )
213chain B and (resseq 15:82 )
313chain C and (resseq 15:82 )
114chain G and (resseq 1:16 )
214chain I and (resseq 1:16 )
314chain K and (resseq 1:16 )
115chain H and (resseq 1:16 )
215chain J and (resseq 1:16 )
315chain L and (resseq 1:16 )

NCS ensembles :
ID
1
2
3
4
5

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Components

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


Mass: 4906.217 Da / Num. of mol.: 3 / Fragment: ARG box DNA segment, strand G / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*TP*GP*CP*AP*TP*CP*GP*TP*TP*AP*TP*GP*CP*AP*A)-3'


Mass: 4888.189 Da / Num. of mol.: 3 / Fragment: ARG box DNA segment, strand H / Source method: obtained synthetically
#4: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H15N4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 3.73 Å3/Da / Density % sol: 67.01 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 86698 / Num. obs: 84444 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 16.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.9 / Num. unique all: 8608 / Rsym value: 0.424 / % possible all: 98.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.automr)model building
PHENIX(phenix.refine: 1.4_58)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ere

3ere


Resolution: 2.306→39.237 Å / SU ML: 0.27 / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 4219 5 %
Rwork0.1838 --
obs0.185 84429 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.496 Å2 / ksol: 0.359 e/Å3
Refinement stepCycle: LAST / Resolution: 2.306→39.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6571 1950 72 435 9028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0138869
X-RAY DIFFRACTIONf_angle_d1.7412428
X-RAY DIFFRACTIONf_dihedral_angle_d22.0923386
X-RAY DIFFRACTIONf_chiral_restr0.091490
X-RAY DIFFRACTIONf_plane_restr0.0061313
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11F1112X-RAY DIFFRACTIONPOSITIONAL
12E1112X-RAY DIFFRACTIONPOSITIONAL0.106
13D1112X-RAY DIFFRACTIONPOSITIONAL0.051
21B583X-RAY DIFFRACTIONPOSITIONAL
22A583X-RAY DIFFRACTIONPOSITIONAL0.135
23C583X-RAY DIFFRACTIONPOSITIONAL0.144
31A492X-RAY DIFFRACTIONPOSITIONAL
32B492X-RAY DIFFRACTIONPOSITIONAL0.035
33C492X-RAY DIFFRACTIONPOSITIONAL0.033
41G326X-RAY DIFFRACTIONPOSITIONAL
42I326X-RAY DIFFRACTIONPOSITIONAL0.035
43K326X-RAY DIFFRACTIONPOSITIONAL0.032
51H324X-RAY DIFFRACTIONPOSITIONAL
52J324X-RAY DIFFRACTIONPOSITIONAL0.035
53L324X-RAY DIFFRACTIONPOSITIONAL0.033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3062-2.33240.32121090.2872383X-RAY DIFFRACTION85
2.3324-2.35980.30481440.27242654X-RAY DIFFRACTION99
2.3598-2.38860.28081570.26382704X-RAY DIFFRACTION98
2.3886-2.41880.31521520.26662708X-RAY DIFFRACTION99
2.4188-2.45070.27611310.25052709X-RAY DIFFRACTION99
2.4507-2.48420.27081460.24572726X-RAY DIFFRACTION99
2.4842-2.51970.2581400.22762711X-RAY DIFFRACTION99
2.5197-2.55730.271370.23262698X-RAY DIFFRACTION99
2.5573-2.59730.30191380.21742705X-RAY DIFFRACTION99
2.5973-2.63990.26391600.21332687X-RAY DIFFRACTION98
2.6399-2.68540.25531300.2082738X-RAY DIFFRACTION98
2.6854-2.73420.23731420.21032692X-RAY DIFFRACTION98
2.7342-2.78680.27191410.20432698X-RAY DIFFRACTION99
2.7868-2.84360.25111140.20422720X-RAY DIFFRACTION98
2.8436-2.90540.26561490.20752746X-RAY DIFFRACTION98
2.9054-2.9730.24511310.20312693X-RAY DIFFRACTION98
2.973-3.04730.21891550.19882697X-RAY DIFFRACTION98
3.0473-3.12970.26881440.20512682X-RAY DIFFRACTION98
3.1297-3.22170.20541420.18712689X-RAY DIFFRACTION97
3.2217-3.32570.20381410.17662709X-RAY DIFFRACTION98
3.3257-3.44450.22251420.17762691X-RAY DIFFRACTION98
3.4445-3.58230.19611400.17662710X-RAY DIFFRACTION98
3.5823-3.74520.20351360.17232644X-RAY DIFFRACTION97
3.7452-3.94250.17991480.15892730X-RAY DIFFRACTION97
3.9425-4.18920.16591370.15462646X-RAY DIFFRACTION97
4.1892-4.51230.16271520.14252650X-RAY DIFFRACTION96
4.5123-4.96550.17321250.14072645X-RAY DIFFRACTION95
4.9655-5.68220.13831540.14812645X-RAY DIFFRACTION95
5.6822-7.15190.18131450.16462699X-RAY DIFFRACTION97
7.1519-39.24280.15951370.15822401X-RAY DIFFRACTION85

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