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

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Basic information

Entry
Database: PDB / ID: 2vbw
TitleFeast or famine regulatory protein (Rv3291c)from M. tuberculosis complexed with L-Phenylalanine
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN
KeywordsDNA BINDING PROTEIN / M. TUBERCULOSIS / PHENYLALANINE 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 / 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 / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / 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 / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / 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
PHENYLALANINE / Leucine-responsive regulatory protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.2 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
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)33,2263
Polymers33,0612
Non-polymers1651
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-29.7 kcal/mol
Surface area17660 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.954, 100.954, 99.307
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-2029-

HOH

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Components

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


Mass: 16530.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RV3291C COMPLEXED TO L-PHENYLALANINE / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96896
#2: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 3.84 Å3/Da / Density % sol: 67.68 % / Description: NONE

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / 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: 2.2→20 Å / Num. obs: 26683 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

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

Resolution: 2.2→71.43 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.173 / 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
Rfree0.254 1342 5 %RANDOM
Rwork0.211 ---
obs0.213 25298 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.2→71.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 12 105 2356
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 99
Rwork0.271 1818

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