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- PDB-1hy5: CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF YOPE-YERSINIA PESTIS... -

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Basic information

Entry
Database: PDB / ID: 1hy5
TitleCRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF YOPE-YERSINIA PESTIS GAP EFFECTOR PROTEIN.
ComponentsYERSINIA PESTIS VIRULENCE PROTEIN YOPE
KeywordsTOXIN / four helix up-down-up-down antiparallel bundle / beta hairpin / arginine finger
Function / homology
Function and homology information


symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / negative regulation of phagocytosis / GTPase activator activity / cell outer membrane
Similarity search - Function
YopE, N-terminal domain / YopE, N terminal / Virulence factor YopE uncharacterised domain / Bacterial Rho GTPase-activating protein (GAP) domain profile. / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Outer membrane virulence protein YopE
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.25 Å
AuthorsEvdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Waugh, D.S.
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal structure of the Yersinia pestis GTPase activator YopE.
Authors: Evdokimov, A.G. / Tropea, J.E. / Routzahn, K.M. / Waugh, D.S.
History
DepositionJan 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YERSINIA PESTIS VIRULENCE PROTEIN YOPE
B: YERSINIA PESTIS VIRULENCE PROTEIN YOPE


Theoretical massNumber of molelcules
Total (without water)29,5292
Polymers29,5292
Non-polymers00
Water1,20767
1
A: YERSINIA PESTIS VIRULENCE PROTEIN YOPE


Theoretical massNumber of molelcules
Total (without water)14,7651
Polymers14,7651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YERSINIA PESTIS VIRULENCE PROTEIN YOPE


Theoretical massNumber of molelcules
Total (without water)14,7651
Polymers14,7651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.692, 71.978, 62.684
Angle α, β, γ (deg.)90.00, 113.06, 90.00
Int Tables number5
Space group name H-MC121
Detailsbiological assembly is a monomer - crystal AU contains a dimer. RMSD of the Ca positions within the dimer is 0.34 A

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Components

#1: Protein YERSINIA PESTIS VIRULENCE PROTEIN YOPE / YOPE / YERSINIA OUTER PROTEIN E


Mass: 14764.720 Da / Num. of mol.: 2
Fragment: C-TERMINAL DOMAIN (RESIDUES 90-219); BACTERIAL GTPASE ACTIVATING PROTEIN (GAP DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: YOPE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL)DE3 / References: UniProt: P31493
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.52 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Ammonium sulphate, bicine, potassium nitrate, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2-1.6 Mammonium sulfate1reservoir
2100 mMHEPES1reservoirpH7.0(or Bicine pH9.0)
3100-200 mMpotassium nitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 5, 2000 / Details: osmic mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→100 Å / Num. all: 22062 / Num. obs: 18478 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4 / Num. unique all: 2291 / % possible all: 96.2
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 22062 / % possible obs: 98.9 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 96.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameClassification
SOLVEphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.25→100 Å
Isotropic thermal model: isotropic individual atomic B factors
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh-Huber
Details: Refinement on unmerged Friedel opposites (due to small but tangible selenium anomalous contribution). Refinement by conjugated-gradient least-squares. Selenomethionine restraints derived ...Details: Refinement on unmerged Friedel opposites (due to small but tangible selenium anomalous contribution). Refinement by conjugated-gradient least-squares. Selenomethionine restraints derived from Hic-Up. Two monomers were restrained by NCS (1,4-restraints generated by NCSY in SHELXL). Removal of the NCS restraints does not result in significant changes in the model. The structure was refined using home data (wavelength 1.5418).
RfactorNum. reflection% reflectionSelection details
Rfree0.2383 1665 -random
Rwork0.1967 ---
all0.1978 22062 --
obs0.1761 18478 96 %-
Solvent computationSolvent model: Babinet (SHELXL) / Bsol: 250.018 Å2 / ksol: 0.879 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-0.9624 Å23.0606 Å2-0.4784 Å2
2--0 Å2-0.5418 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.25→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 0 67 1843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_from_restr_planes0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.031
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.4
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg16.5
X-RAY DIFFRACTIONs_improper_angle_d0.03
X-RAY DIFFRACTIONs_plane_restr0.02

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