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- PDB-1k6z: Crystal Structure of the Yersinia Secretion Chaperone SycE -

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Basic information

Entry
Database: PDB / ID: 1k6z
TitleCrystal Structure of the Yersinia Secretion Chaperone SycE
ComponentsType III secretion chaperone SycE
KeywordsCHAPERONE / secretion / yersinia pestis / toxin
Function / homology
Function and homology information


protein secretion by the type III secretion system
Similarity search - Function
Type III secretion chaperone SycE / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / YopE regulator
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsEvdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Three-dimensional structure of the type III secretion chaperone SycE from Yersinia pestis.
Authors: Evdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Waugh, D.S.
History
DepositionOct 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / struct_conn / 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_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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III secretion chaperone SycE
B: Type III secretion chaperone SycE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7004
Polymers32,5622
Non-polymers1382
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-15 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.879, 56.038, 54.993
Angle α, β, γ (deg.)90.00, 114.04, 90.00
Int Tables number4
Space group name H-MP1211
Detailswe believe that the biological assembly is a dimer, represented in the A.U.

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Components

#1: Protein Type III secretion chaperone SycE / YopE chaperone SycE


Mass: 16280.763 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: SycE / Plasmid: pKM596 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P31491
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 20% PEG8000, 500 mM Imidazole Acetate pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG80001reservoir
2500 mMimidazole acetate1reservoirpH7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9796, 0.9795, 0.9400
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 10, 2001
RadiationMonochromator: X9B silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97951
30.941
ReflectionResolution: 2→35 Å / Num. obs: 16201 / % possible obs: 82 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.92 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.045 / Net I/σ(I): 16.65
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1372 / % possible all: 99
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 30 Å / Num. obs: 21311 / % possible obs: 99.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
SHELXDphasing
SHARPphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: MAD

Resolution: 2→35 Å / Isotropic thermal model: one per atom / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: conjugated-gradient LS procedure in SHELXL
RfactorNum. reflection% reflectionSelection details
Rfree0.248 955 4.8 %random
Rwork0.194 ---
all-19757 --
obs-19757 --
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 10 194 2161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_zero_chiral_vol0.024
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 35 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.1
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg18.5
X-RAY DIFFRACTIONs_plane_restr0.02

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