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- PDB-3e3c: Structure of GrlR-lipid complex -

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Basic information

Entry
Database: PDB / ID: 3e3c
TitleStructure of GrlR-lipid complex
ComponentsL0044
KeywordsLIPID BINDING PROTEIN / GrlR / LEE regulator / lipid binding
Function / homologyT3SS negative regulator GrlR / T3SS negative regulator GrlR domain superfamily / Lipocalin / Beta Barrel / Mainly Beta / (2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL HEXANOATE / L0044 / GrlR
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJobichen, C. / Sivaraman, J.
CitationJournal: Biochem.J. / Year: 2009
Title: Identification and characterization of the lipid binding property of GrlR, a locus of enterocyte effacement regulator.
Authors: Jobichen, C. / Fernandis, A.Z. / Velazquez-Campoy, A. / Leung, K.Y. / Mok, Y.K. / Wenk, M.R. / Sivaraman, J.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L0044
B: L0044
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0114
Polymers26,4702
Non-polymers5402
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-18 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.729, 66.015, 83.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L0044


Mass: 13235.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: ECs4578 / Plasmid: pETM32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O85638, UniProt: Q7DB61*PLUS
#2: Chemical ChemComp-HHG / (2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL HEXANOATE / 1-MONOHEXANOYL-2-HYDROXY-SN-GLYCERO-3-PHOSPHATE


Mass: 270.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% ethylene Glycol, 4% Tertiary Butanol, 4% triflouroethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2007 / Details: Mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 8751 / Num. obs: 8472 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.248 / Num. unique all: 781 / % possible all: 89.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OVS

2ovs


Resolution: 2.5→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 507 -Random
Rwork0.2309 ---
obs0.2309 8472 97 %-
all-8751 --
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 34 264 2134
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_bond_d0.01

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