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- PDB-3eb8: VirA -

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Basic information

Entry
Database: PDB / ID: 3eb8
TitleVirA
ComponentsCysteine protease-like virA
KeywordsHYDROLASE / beta sheet / alpha helix / Protease / Secreted / Thiol protease / Virulence
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
EspG protein, N-terminal domain / Cysteine protease, VirA/EspG / Cysteine protease, VirA/EspG, N-terminal / EspG protein / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Cysteine protease-like VirA
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsGermane, K.L. / Spiller, B.W.
CitationJournal: Biochemistry / Year: 2008
Title: Structural and functional studies indicate that Shigella VirA is not a protease and does not directly destabilize microtubules.
Authors: Germane, K.L. / Ohi, R. / Goldberg, M.B. / Spiller, B.W.
History
DepositionAug 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine protease-like virA
B: Cysteine protease-like virA


Theoretical massNumber of molelcules
Total (without water)79,7462
Polymers79,7462
Non-polymers00
Water1,63991
1
A: Cysteine protease-like virA


Theoretical massNumber of molelcules
Total (without water)39,8731
Polymers39,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Cysteine protease-like virA


Theoretical massNumber of molelcules
Total (without water)39,8731
Polymers39,8731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Cysteine protease-like virA

B: Cysteine protease-like virA


Theoretical massNumber of molelcules
Total (without water)79,7462
Polymers79,7462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_655-y+1,-x,-z+1/21
Buried area3090 Å2
ΔGint-25 kcal/mol
Surface area30280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.290, 91.290, 198.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cysteine protease-like virA / Effector protein virA


Mass: 39872.914 Da / Num. of mol.: 2 / Fragment: delta44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: virA, CP0181, pWR501_0191 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)
References: UniProt: Q7BU69, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.51 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 33386 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 59.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 27
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.07 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→39.99 Å / SU ML: 0.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1658 4.97 %
Rwork0.217 --
obs0.22 33386 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.18 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 62.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.0475 Å20 Å20 Å2
2--0.0475 Å20 Å2
3----0.095 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5280 0 0 91 5371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47230.34251480.26312504X-RAY DIFFRACTION98
2.4723-2.55210.35581290.25082577X-RAY DIFFRACTION99
2.5521-2.64330.30061340.25122599X-RAY DIFFRACTION99
2.6433-2.74910.36221340.24322606X-RAY DIFFRACTION99
2.7491-2.87410.3661530.25452607X-RAY DIFFRACTION100
2.8741-3.02560.3071390.25662599X-RAY DIFFRACTION100
3.0256-3.21510.30291280.24062647X-RAY DIFFRACTION100
3.2151-3.46320.25521380.22922645X-RAY DIFFRACTION100
3.4632-3.81150.27821310.20972670X-RAY DIFFRACTION100
3.8115-4.36240.19491340.17412683X-RAY DIFFRACTION100
4.3624-5.4940.21271390.17492718X-RAY DIFFRACTION100
5.494-39.99290.25811510.21212873X-RAY DIFFRACTION100

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