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- PDB-1l2w: Crystal Structure of the Yersinia Virulence Effector YopE Chapero... -

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Basic information

Entry
Database: PDB / ID: 1l2w
TitleCrystal Structure of the Yersinia Virulence Effector YopE Chaperone-binding Domain in Complex with its Secretion Chaperone, SycE
Components
  • Outer membrane virulence protein yopE
  • YopE regulator
KeywordsCHAPERONE / CHAPERONE AND VIRULENCE PROTEIN
Function / homology
Function and homology information


protein secretion by the type III secretion system / negative regulation of phagocytosis / GTPase activator activity / cell outer membrane
Similarity search - Function
YopE, N-terminal domain / YopE, N terminal / Type III secretion chaperone SycE / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Tir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / Yope Regulator; Chain: A, - #10 ...YopE, N-terminal domain / YopE, N terminal / Type III secretion chaperone SycE / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / 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
YopE regulator / Outer membrane virulence protein YopE
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBirtalan, S.C. / Phillips, R.M. / Ghosh, P.
CitationJournal: Mol.Cell / Year: 2002
Title: Three-dimensional secretion signals in chaperone-effector complexes of bacterial pathogens.
Authors: Birtalan, S.C. / Phillips, R.M. / Ghosh, P.
History
DepositionFeb 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE SEQUENCE OF THE SYCE PROTEIN, CHAINS A-H, MATCHES SWISS PROT ENTRY P31491, WHOSE ...SEQUENCE THE SEQUENCE OF THE SYCE PROTEIN, CHAINS A-H, MATCHES SWISS PROT ENTRY P31491, WHOSE SOURCE IS YERSINIA PESTIS. THE SOURCE OF THE SYCE PROTEIN IN THIS ENTRY IS YERSINIA PSEUDOTUBERCULOSIS. THERE IS AN EXTRA GLYCINE, RESIDUE 1, IN CHAINS A-H WHICH WAS INSERTED FOR CLONING PURPOSES, and the last 8 residues were cleaved to yield residues 0-122. The N- and C- terminal residues of chains I-L were cleaved to yield residues 17-85.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YopE regulator
B: YopE regulator
C: YopE regulator
D: YopE regulator
E: YopE regulator
F: YopE regulator
G: YopE regulator
H: YopE regulator
I: Outer membrane virulence protein yopE
J: Outer membrane virulence protein yopE
K: Outer membrane virulence protein yopE
L: Outer membrane virulence protein yopE


Theoretical massNumber of molelcules
Total (without water)139,86112
Polymers139,86112
Non-polymers00
Water6,521362
1
A: YopE regulator
B: YopE regulator
I: Outer membrane virulence protein yopE


Theoretical massNumber of molelcules
Total (without water)34,9653
Polymers34,9653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-47 kcal/mol
Surface area13650 Å2
MethodPISA
2
C: YopE regulator
D: YopE regulator
J: Outer membrane virulence protein yopE


Theoretical massNumber of molelcules
Total (without water)34,9653
Polymers34,9653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-46 kcal/mol
Surface area13590 Å2
MethodPISA
3
E: YopE regulator
F: YopE regulator
K: Outer membrane virulence protein yopE


Theoretical massNumber of molelcules
Total (without water)34,9653
Polymers34,9653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-45 kcal/mol
Surface area13390 Å2
MethodPISA
4
G: YopE regulator
H: YopE regulator
L: Outer membrane virulence protein yopE


Theoretical massNumber of molelcules
Total (without water)34,9653
Polymers34,9653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-45 kcal/mol
Surface area13370 Å2
MethodPISA
5
C: YopE regulator
D: YopE regulator
G: YopE regulator
H: YopE regulator
J: Outer membrane virulence protein yopE
L: Outer membrane virulence protein yopE


Theoretical massNumber of molelcules
Total (without water)69,9306
Polymers69,9306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16950 Å2
ΔGint-101 kcal/mol
Surface area24940 Å2
MethodPISA
6
A: YopE regulator
B: YopE regulator
I: Outer membrane virulence protein yopE

E: YopE regulator
F: YopE regulator
K: Outer membrane virulence protein yopE


Theoretical massNumber of molelcules
Total (without water)69,9306
Polymers69,9306
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area16970 Å2
ΔGint-102 kcal/mol
Surface area25050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.845, 73.352, 74.263
Angle α, β, γ (deg.)103.37, 109.18, 107.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
YopE regulator / YOPE CHAPERONE SYCE


Mass: 13843.607 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: syce / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0N9NJF3*PLUS
#2: Protein
Outer membrane virulence protein yopE


Mass: 7277.952 Da / Num. of mol.: 4 / Fragment: Chaperone-binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: yope / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08008
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 8000, sodium tartrate, sodium acetate, dithiothreitol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1120 mg/mlprotein11
210 mMTris11pH8.0
31 mMdithiothreitol11
418 %(w/v)PEG800012
550 mMsodium tartrate12
6100 mMsodium acetate12pH4.6
71 mMdithiothreitol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. all: 87145 / Num. obs: 84804 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 36.69 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 18.22
Reflection shellResolution: 1.99→2.03 Å / Redundancy: 2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.77 / Num. unique all: 4425 / Rsym value: 0.46 / % possible all: 96.5
Reflection
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 20 Å / % possible obs: 96.7 %
Reflection shell
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 2.07 Å / % possible obs: 96.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jya

1jya


Resolution: 2→20 Å / Isotropic thermal model: atomic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 4252 -random 5%
Rwork0.251 ---
all-84845 --
obs-84804 97.3 %-
Displacement parametersBiso mean: 48.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å22.387 Å25.289 Å2
2--1.204 Å2-1.036 Å2
3----3.013 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9232 0 0 362 9594
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.15
X-RAY DIFFRACTIONc_dihedral_angle_d22.74
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.3828 404 -
Rwork0.3497 --
obs-7992 91.9 %
Refinement
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 20 Å / Num. reflection obs: 77053 / Num. reflection Rfree: 4091 / % reflection Rfree: 5 % / Rfactor obs: 0.249 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.16
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.74
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor obs: 0.3497

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