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

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Basic information

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


amino acid binding / response to amino acid / protein homooligomerization / sequence-specific DNA binding / DNA binding / cytosol
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
TYROSINE / Leucine-responsive regulatory protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.8 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 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,2423
Polymers33,0612
Non-polymers1811
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-29.5 kcal/mol
Surface area17850 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.810, 100.810, 99.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsL-TYROSINE (TYR): L-TYROSINE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.96 Å3/Da / Density % sol: 68.69 % / Description: NONE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 12768 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.8→71.25 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.325 / 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
Rfree0.261 631 5 %RANDOM
Rwork0.202 ---
obs0.205 12103 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.8→71.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 13 26 2277
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.405 72
Rwork0.309 861

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