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- PDB-2ovs: Crystal structure of a Type Three secretion System protein -

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Basic information

Entry
Database: PDB / ID: 2ovs
TitleCrystal structure of a Type Three secretion System protein
ComponentsL0044
KeywordsGENE REGULATION / LIGAND BINDING PROTEIN / Global Regulator protein Type three Secretion System
Function / homologyT3SS negative regulator GrlR / T3SS negative regulator GrlR domain superfamily / Lipocalin / Beta Barrel / Mainly Beta / L0044
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJobichen, C. / Li, M. / Sivaraman, J.
CitationJournal: Plos Pathog. / Year: 2007
Title: Structure of GrlR and the implication of its EDED motif in mediating the regulation of type III secretion system in EHEC.
Authors: Jobichen, C. / Li, M. / Yerushalmi, G. / Tan, Y.W. / Mok, Y.K. / Rosenshine, I. / Leung, K.Y. / Sivaraman, J.
History
DepositionFeb 15, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2020Group: Database references / Derived calculations / Structure summary
Category: struct / struct_conn ...struct / struct_conn / struct_ref_seq_dif / struct_site
Item: _struct.title / _struct_conn.pdbx_leaving_atom_flag ..._struct.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: L0044
B: L0044
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1404
Polymers26,7522
Non-polymers3882
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-5 kcal/mol
Surface area11340 Å2
MethodPISA
2
A: L0044
hetero molecules

B: L0044
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1404
Polymers26,7522
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area2710 Å2
ΔGint-5 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.835, 66.092, 83.577
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 / Orf10


Mass: 13375.815 Da / Num. of mol.: 2 / Fragment: residues (-6)-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EHEC / Gene: Orf10 / Plasmid: pETM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O85638
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.63 %
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: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2005 / Details: Mirrors
RadiationMonochromator: Selenium / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 19580 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.148 / Rsym value: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 14.8 / Num. unique all: 4134 / Rsym value: 0.354 / % possible all: 90.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.69 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1722 -Random
Rwork0.215 ---
obs0.215 19580 92.9 %-
all-19580 --
Displacement parametersBiso mean: 4.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 26 342 2204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.3 167 -
Rwork0.291 --
obs-4134 69.9 %

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