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- PDB-2gqq: Crystal Structure of E. coli Leucine-responsive regulatory protei... -

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Basic information

Entry
Database: PDB / ID: 2gqq
TitleCrystal Structure of E. coli Leucine-responsive regulatory protein (Lrp)
ComponentsLeucine-responsive regulatory protein
KeywordsTRANSCRIPTION / helix-turn-helix
Function / homology
Function and homology information


alanine catabolic process / response to L-leucine / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / identical protein binding / cytosol
Similarity search - Function
Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / 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 ...Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / 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 / ArsR-like helix-turn-helix domain / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.2 Å
Authorsde los Rios, S. / Perona, J.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure of the Escherichia coli Leucine-responsive Regulatory Protein Lrp Reveals a Novel Octameric Assembly.
Authors: de Los Rios, S. / Perona, J.J.
History
DepositionApr 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-responsive regulatory protein
B: Leucine-responsive regulatory protein
C: Leucine-responsive regulatory protein
D: Leucine-responsive regulatory protein


Theoretical massNumber of molelcules
Total (without water)75,1344
Polymers75,1344
Non-polymers00
Water00
1
A: Leucine-responsive regulatory protein
B: Leucine-responsive regulatory protein
C: Leucine-responsive regulatory protein
D: Leucine-responsive regulatory protein

A: Leucine-responsive regulatory protein
B: Leucine-responsive regulatory protein
C: Leucine-responsive regulatory protein
D: Leucine-responsive regulatory protein


Theoretical massNumber of molelcules
Total (without water)150,2698
Polymers150,2698
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area26870 Å2
ΔGint-189 kcal/mol
Surface area54080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.100, 237.000, 75.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe octamer is generated from the tetramer along the 2-fold axis:

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Components

#1: Protein
Leucine-responsive regulatory protein


Mass: 18783.600 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lrp, alsB, ihb, livR, oppI / Plasmid: pJWD1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P0ACJ0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.05M MES pH 5.6, 0.01M magnesium chloride, 0.4M potassium chloride, 9% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL7-111.08
SYNCHROTRONSSRL BL11-320.975
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJun 1, 2001
ADSC QUANTUM 42CCDJul 2, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
20.9751
ReflectionResolution: 3.2→30 Å / Num. all: 15200 / Num. obs: 15185 / % possible obs: 99.9 % / Observed criterion σ(F): 15.65 / Observed criterion σ(I): 6.7 / Redundancy: 4 %
Reflection shellResolution: 3.2→3.27 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 3.2→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.322 1406 random
Rwork0.267 --
all0.322 15200 -
obs0.322 13800 -
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 0 0 4342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

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