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- PDB-3ee1: Novel fold of VirA, a type III secretion system effector protein ... -

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Basic information

Entry
Database: PDB / ID: 3ee1
TitleNovel fold of VirA, a type III secretion system effector protein from Shigella flexneri
ComponentsEffector protein virA
KeywordsHYDROLASE / beta barrels / six-stranded beta barrel / 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 / Resolution: 3.01 Å
AuthorsDavis, J.S.
CitationJournal: Protein Sci. / Year: 2008
Title: Novel fold of VirA, a type III secretion system effector protein from Shigella flexneri
Authors: Davis, J. / Wang, J. / Tropea, J.E. / Zhang, D. / Dauter, Z. / Waugh, D.S. / Wlodawer, A.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Effector protein virA
B: Effector protein virA


Theoretical massNumber of molelcules
Total (without water)89,7332
Polymers89,7332
Non-polymers00
Water00
1
A: Effector protein virA


Theoretical massNumber of molelcules
Total (without water)44,8671
Polymers44,8671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Effector protein virA


Theoretical massNumber of molelcules
Total (without water)44,8671
Polymers44,8671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.252, 170.910, 46.165
Angle α, β, γ (deg.)90.00, 104.89, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 1:13 or resseq 58:310 or resseq 315:328 or resseq 339:399
21chain B and (resseq 1:13 or resseq 58:310 or resseq 315:328 or resseq 339:399

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUVALVALAA1 - 131 - 13
12GLUGLUGLUGLUAA58 - 31058 - 310
13ASNASNPROPROAA315 - 328315 - 328
14GLYGLYASPASPAA339 - 399339 - 399
21GLUGLUVALVALBB1 - 131 - 13
22GLUGLUGLUGLUBB58 - 31058 - 310
23ASNASNPROPROBB315 - 328315 - 328
24GLYGLYASPASPBB339 - 399339 - 399

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Components

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


Mass: 44866.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: virA / Production host: Escherichia coli (E. coli)
References: UniProt: Q7BU69, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
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: 3.19 Å3/Da / Density % sol: 61.46 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 21471 / % possible obs: 96.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.082
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3-3.1160.421180.5
3.11-3.236.50.341189.7
3.23-3.386.70.259197.7
3.38-3.567.20.187199.6
3.56-3.787.40.1371100
3.78-4.077.50.1071100
4.07-4.487.40.0791100
4.48-5.127.40.0711100
5.12-6.447.40.0771100
6.44-307.30.06199.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 3.01→28.631 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0.57 / SU ML: 0.31 / σ(F): 1.35 / Phase error: 27.25 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2556 1096 5.11 %
Rwork0.2136 --
obs0.2157 21459 96.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.308 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 106.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.35 Å2
2---1.39 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 3.01→28.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 0 0 5244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115350
X-RAY DIFFRACTIONf_angle_d1.5297266
X-RAY DIFFRACTIONf_dihedral_angle_d20.5861918
X-RAY DIFFRACTIONf_chiral_restr0.095838
X-RAY DIFFRACTIONf_plane_restr0.006946
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2622X-RAY DIFFRACTIONPOSITIONAL
12B2622X-RAY DIFFRACTIONPOSITIONAL0.047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.01-3.14650.32361140.30882069X-RAY DIFFRACTION78
3.1465-3.31220.37271280.29312454X-RAY DIFFRACTION93
3.3122-3.51940.30111400.26252632X-RAY DIFFRACTION99
3.5194-3.79050.27961490.22472603X-RAY DIFFRACTION100
3.7905-4.17090.26141510.21282648X-RAY DIFFRACTION100
4.1709-4.77210.23281510.17682619X-RAY DIFFRACTION100
4.7721-6.00320.21421340.19022649X-RAY DIFFRACTION100
6.0032-28.63220.22631290.19192689X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2314-0.83242.57950.96311.39420.94180.1648-0.56170.22660.2968-0.05360.1473-0.2510.1417-0.05970.5804-0.09640.08931.02250.0330.487853.45288.037829.5045
21.9417-0.18130.94433.8792-0.61510.37910.0846-0.013-0.1637-0.21620.10550.6261-0.07410.0523-0.14850.61060.0017-0.06040.5578-0.01550.609629.802783.584121.3371
38.6681-4.78163.56545.39161.6974-2.3233-1.6139-3.61741.21272.1451.3579-0.82360.6024-1.7984-0.18560.80060.27420.04261.7415-0.04630.42245.5407125.514335.0372
41.71390.070.19043.4790.21320.3880.1313-0.118-0.0132-0.11990.0458-0.44550.1171-0.22-0.14020.67150.0508-0.130.63060.05280.587128.382123.271122.7613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:171)A1 - 171
2X-RAY DIFFRACTION2(chain A and resid 172:399)A172 - 399
3X-RAY DIFFRACTION3(chain B and resid 1:102)B1 - 102
4X-RAY DIFFRACTION4(chain B and resid 103:399)B103 - 399

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