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- PDB-2w24: M. tuberculosis Rv3291c complexed to Lysine -

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Basic information

Entry
Database: PDB / ID: 2w24
TitleM. tuberculosis Rv3291c complexed to Lysine
ComponentsPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
KeywordsTRANSCRIPTION / RV3291C / DNA-BINDING / LYSINE COMPLEX / TRANSCRIPTION REGULATOR / TRANSCRIPTION REGULATION
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. / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Lrp/AsnC ligand binding domain / Transcription regulator AsnC/Lrp, ligand binding domain / AsnC-type HTH 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. / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Lrp/AsnC ligand binding domain / Transcription regulator AsnC/Lrp, ligand binding domain / AsnC-type HTH 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 / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LYSINE / Leucine-responsive regulatory protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShrivastava, T. / Ramachandran, R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Ligand-Induced Structural Transitions, Mutational Analysis, and 'Open' Quaternary Structure of the M. Tuberculosis Feast/Famine Regulatory Protein (Rv3291C).
Authors: Shrivastava, T. / Dey, A. / Ramachandran, R.
History
DepositionOct 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,2083
Polymers33,0612
Non-polymers1471
Water81145
1
A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
hetero molecules

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
hetero molecules

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
hetero molecules

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,83412
Polymers132,2458
Non-polymers5894
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area32800 Å2
ΔGint-147.97 kcal/mol
Surface area48950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.980, 100.980, 99.311
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 PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN / FEAST OR FAMINE REGULATORY PROTEIN / LEUCINE-RESPONSIVE REGULATORY PROTEIN / RV3291C


Mass: 16530.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Variant: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96896
#2: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.8 Å3/Da / Density % sol: 68.5 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→71.43 Å / Num. obs: 18364 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.29
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IVM

2ivm


Resolution: 2.5→71.43 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 938 5.1 %RANDOM
Rwork0.191 ---
obs0.193 17382 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→71.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 9 45 2293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222276
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.541.9763097
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5265292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50122.427103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.59815374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2751530
X-RAY DIFFRACTIONr_chiral_restr0.2250.2378
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.2842
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21542
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3151.51472
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49922370
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1793804
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.2224.5727
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.395 82
Rwork0.296 1245

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