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- PDB-2vc0: Feast or famine regulatory protein (Rv3291c)from M. tuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 2vc0
TitleFeast or famine regulatory protein (Rv3291c)from M. tuberculosis complexed with L-Leucine
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN
KeywordsDNA BINDING PROTEIN / FEAST/FAMINE REGULATORY PROTEIN / DNA-BINDING PROTEIN / M. TUBERCULOSIS / LEUCINE COMPLEX / TRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATION / LRP / RV3291C / DNA-BINDING / TRANSCRIPTION
Function / homology
Function and homology information


amino acid binding / protein homooligomerization / sequence-specific DNA binding / DNA binding
Similarity search - Function
AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LEUCINE / Leucine-responsive regulatory protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.5 Å
AuthorsShrivastava, T. / Ramachandran, R.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Mechanistic insights from the crystal structures of a feast/famine regulatory protein from Mycobacterium tuberculosis H37Rv.
Authors: Shrivastava, T. / Ramachandran, R.
History
DepositionSep 18, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation
Category: atom_site / citation / exptl_crystal_grow
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1Oct 9, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 2.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATORY PROTEIN
B: TRANSCRIPTIONAL REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1923
Polymers33,0612
Non-polymers1311
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-31.4 kcal/mol
Surface area17830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.875, 100.875, 99.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-2008-

HOH

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Components

#1: Protein TRANSCRIPTIONAL REGULATORY PROTEIN / RV3291C / ASNC-FAMILY / LEUCINE-RESPONSIVE REGULATORY PROTEIN


Mass: 16530.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P96896
#2: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-LEUCINE (LEU): L-LEUCINE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.48 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 64899 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.3 / % possible all: 98.3

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.5→71.25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3 ARE DISORDERED IN THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.257 890 5.1 %RANDOM
Rwork0.212 ---
obs0.214 16501 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→71.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 9 46 2293
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 70
Rwork0.342 1226

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