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- PDB-1xou: Crystal structure of the CesA-EspA complex -

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Basic information

Entry
Database: PDB / ID: 1xou
TitleCrystal structure of the CesA-EspA complex
Components
  • EspA
  • Z5138 gene product
KeywordsStructural protein/chaperone / coiled coil / helix bundle / heterodimer / Structural protein-chaperone COMPLEX
Function / homology
Function and homology information


EspA/CesA-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Type III secretion system filament chaperone CesA / Type III secretion system filament chaperone CesA / EspA-like secreted protein / EspA-like secreted protein / EspA/CesA-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special ...EspA/CesA-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / Type III secretion system filament chaperone CesA / Type III secretion system filament chaperone CesA / EspA-like secreted protein / EspA-like secreted protein / EspA/CesA-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsYip, C.K. / Finlay, B.B. / Strynadka, N.C.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Structural characterization of a type III secretion system filament protein in complex with its chaperone.
Authors: Yip, C.K. / Finlay, B.B. / Strynadka, N.C.J.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EspA
B: Z5138 gene product


Theoretical massNumber of molelcules
Total (without water)31,7132
Polymers31,7132
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-49 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.422, 72.383, 95.679
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 EspA


Mass: 20904.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: espA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q47184
#2: Protein Z5138 gene product


Mass: 10808.205 Da / Num. of mol.: 1 / Mutation: S2G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: orf3 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O52124
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: 1.89 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: PEG 1500, Tris, pH 8.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2004
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→57.73 Å / Num. all: 6480 / Num. obs: 6480 / % possible obs: 100 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8 / Redundancy: 13.1 % / Biso Wilson estimate: 73.4 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 21.5
Reflection shellResolution: 2.8→2.94 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 4.1 / Num. unique all: 930 / Rsym value: 0.507 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→57.73 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 1147616.94 / Data cutoff high rms absF: 1147616.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 362 5.6 %RANDOM
Rwork0.236 ---
all0.24 6480 --
obs0.236 6480 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1325 Å2 / ksol: 0.381881 e/Å3
Displacement parametersBiso mean: 70.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.34 Å20 Å20 Å2
2--20.17 Å20 Å2
3----24.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.8→57.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 0 0 1238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it4.192.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 64 6.1 %
Rwork0.274 990 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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