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- PDB-2qz8: Crystal structure of Mycobacterium tuberculosis Leucine response ... -

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Basic information

Entry
Database: PDB / ID: 2qz8
TitleCrystal structure of Mycobacterium tuberculosis Leucine response regulatory protein (LrpA)
ComponentsProbable transcriptional regulatory protein
KeywordsTRANSCRIPTION / Leucine responsive regulatory protein / HTH motif / Global transcriptional regulator / Structural Genomics / TB Structural Genomics Consortium / TBSGC / PSI / Protein Structure Initiative / DNA-binding / Transcription regulation
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 / 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
Leucine-responsive regulatory protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å
AuthorsManchi, C.M.R. / Gokulan, K. / Ioerger, T. / Jacobs Jr., W.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response.
Authors: Reddy, M.C. / Gokulan, K. / Jacobs, W.R. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable transcriptional regulatory protein
B: Probable transcriptional regulatory protein
C: Probable transcriptional regulatory protein
D: Probable transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)65,7824
Polymers65,7824
Non-polymers00
Water4,774265
1
A: Probable transcriptional regulatory protein
B: Probable transcriptional regulatory protein
C: Probable transcriptional regulatory protein
D: Probable transcriptional regulatory protein

A: Probable transcriptional regulatory protein
B: Probable transcriptional regulatory protein
C: Probable transcriptional regulatory protein
D: Probable transcriptional regulatory protein


Theoretical massNumber of molelcules
Total (without water)131,5648
Polymers131,5648
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area31660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.284, 149.900, 62.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Probable transcriptional regulatory protein / Leucine-responsive regulatory protein


Mass: 16445.492 Da / Num. of mol.: 4 / Mutation: A22V, L108M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: lrp, MT3390, Rv3291c / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P96896
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion / pH: 6
Details: 70mM Sodium acetate, 20% Glycerol, 5.6% PEG 4000, pH 6.0, VAPOR DIFFUSION, temperature 291.5K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.96400, 1.00000
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2003
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9641
211
ReflectionResolution: 2.16→105.41 Å / Num. obs: 67785 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.88 % / Biso Wilson estimate: 27.273 Å2 / Rsym value: 0.0261 / Net I/σ(I): 30.1
Reflection shellResolution: 2.16→2.26 Å / Redundancy: 1.73 % / Rmerge(I) obs: 0.0521 / Mean I/σ(I) obs: 16.7 / Rsym value: 0.055 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIXrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.16→29.09 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.495 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing and refinement. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program REFMAC 5.2.0005 has also been used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 3781 5.58 %RANDOM
Rwork0.2156 ---
obs0.2156 67785 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.16→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 0 265 4797
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetWeight
X-RAY DIFFRACTIONf_bond_d0.0050466.971
X-RAY DIFFRACTIONf_angle_deg0.74301610.699
X-RAY DIFFRACTIONf_angle_deg_na
X-RAY DIFFRACTIONf_angle_deg_prot
X-RAY DIFFRACTIONf_dihedral_angle_d11.0560.012216.139
X-RAY DIFFRACTIONf_dihedral_angle_d_na
X-RAY DIFFRACTIONf_dihedral_angle_d_prot
X-RAY DIFFRACTIONf_improper_angle_d
X-RAY DIFFRACTIONf_improper_angle_d_na
X-RAY DIFFRACTIONf_improper_angle_d_prot
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it
LS refinement shellResolution: 2.16→2.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.2368 39 -
obs--7 %

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