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- PDB-4lk4: Structure of Vibrio cholerae VesB protease -

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Basic information

Entry
Database: PDB / ID: 4lk4
TitleStructure of Vibrio cholerae VesB protease
ComponentsVESB protease
KeywordsHYDROLASE / trypsin / peptidase S1 family / endopeptidase / DUF3466 / secreted protein / extracellular
Function / homology
Function and homology information


serine-type peptidase activity / membrane => GO:0016020 / serine-type endopeptidase activity / proteolysis
Similarity search - Function
GlyGly-CTERM domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...GlyGly-CTERM domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 2.4 Å
AuthorsKorotkov, K.V. / Delarosa, J.R. / Hol, W.G.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Functional and Structural Characterization of Vibrio cholerae Extracellular Serine Protease B, VesB.
Authors: Gadwal, S. / Korotkov, K.V. / Delarosa, J.R. / Hol, W.G. / Sandkvist, M.
History
DepositionJul 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: VESB protease


Theoretical massNumber of molelcules
Total (without water)38,4211
Polymers38,4211
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.570, 121.570, 71.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-428-

HOH

21A-448-

HOH

31A-467-

HOH

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Components

#1: Protein VESB protease / VC1200


Mass: 38420.602 Da / Num. of mol.: 1 / Fragment: UNP residues 24-373 / Mutation: S221A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: 569B / Gene: VC1200 / Plasmid: pCDF-22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9KSQ6, Hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Tris-HCl, pH 9.0, 3.0 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→46.3 Å / Num. all: 21460 / Num. obs: 21358 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.31 % / Biso Wilson estimate: 56.776 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.4-2.466.481.0732.33100401550155099.9
2.46-2.530.8962.799091518100
2.53-2.60.6773.5795451471100
2.6-2.680.4964.7592741427100
2.68-2.770.4095.749092140499.9
2.77-2.870.3037.468714134999.9
2.87-2.980.239.128396130399.8
2.98-3.10.15213.388065125399.9
3.1-3.240.10417.87786121499.9
3.24-3.390.07922.017342115499.4
3.39-3.580.05927.986939110199.5
3.58-3.790.04733.726562105099.5
3.79-4.060.0437.85603597899.3
4.06-4.380.03244.21564092199.2
4.38-4.80.02947.37509184598.6
4.8-5.370.02747.07453877999.2
5.37-6.20.02846.44415269198.3
6.2-7.590.02648.35353959498.7
7.59-10.730.01955.6276047398.1
10.730.02353.29141728395

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
BOSdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: molecular replacement-SAD
Starting model: PDB ENTRY 1EAX

1eax


Resolution: 2.4→46.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2208 / WRfactor Rwork: 0.1749 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8395 / SU B: 13.979 / SU ML: 0.163 / SU R Cruickshank DPI: 0.2307 / SU Rfree: 0.2051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1070 5 %RANDOM
Rwork0.1872 ---
obs0.1896 20306 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.44 Å2 / Biso mean: 59.7818 Å2 / Biso min: 29.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 0 93 2558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192514
X-RAY DIFFRACTIONr_bond_other_d0.0010.022328
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9413424
X-RAY DIFFRACTIONr_angle_other_deg0.7813.0025326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1535322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66424.273110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36615383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1441514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
X-RAY DIFFRACTIONr_mcbond_it1.1912.2551300
X-RAY DIFFRACTIONr_mcbond_other1.1922.2551299
X-RAY DIFFRACTIONr_mcangle_it1.9413.3831618
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 76 -
Rwork0.274 1471 -
all-1547 -
obs--99.87 %
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)
15.2082-0.5203-0.85723.3848-1.11244.5133-0.00740.1067-0.1723-0.29410.0113-0.04530.34390.4846-0.00390.39440.0341-0.01780.3060.00080.065530.09714.1574.888
22.3523-0.05640.34241.703-0.56472.815-0.0477-0.1838-0.2334-0.03620.14460.09710.19010.0401-0.09690.34210.07620.03550.31050.04010.077731.3611.7415.938
315.4857-4.83380.21732.4574-0.40450.35460.32620.32180.5115-0.3222-0.0519-0.0963-0.13390.0609-0.27430.6037-0.04380.12630.4948-0.04450.310430.70320.342.942
44.20012.9065-0.94024.31640.96197.78910.1114-0.22940.2739-0.16610.11010.0244-0.62990.9762-0.22150.3325-0.03610.10340.5664-0.05840.145149.54421.53413.795
55.74410.8162-1.36762.3323-1.84271.56960.06360.1402-0.2951-0.1701-0.0891-0.02350.14360.11680.02540.39770.12270.01810.4821-0.0170.080440.24113.1829.604
61.76621.08183.71080.90762.57458.1906-0.0794-0.1762-0.1193-0.31450.529-0.2628-0.63430.326-0.44961.1577-0.11920.4221.9744-0.30991.192139.88530.50510.03
71.6992-0.5224-0.41581.08970.16514.0522-0.0602-0.4423-0.09710.16980.26360.14890.06220.098-0.20340.3310.15090.04140.43320.09220.084836.79211.43127.146
83.6947-0.43050.91375.18110.39747.6624-0.4957-1.2508-0.52640.5090.52040.49320.63220.0584-0.02480.44670.26810.15130.80580.33480.157930.9670.99341.913
93.1044-0.2004-0.85467.92611.98845.2892-0.2268-1.0341-0.06440.37930.4199-0.042-0.02860.0379-0.19310.46710.27860.07680.76370.20480.094533.828.51240.792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 55
2X-RAY DIFFRACTION2A56 - 162
3X-RAY DIFFRACTION3A163 - 182
4X-RAY DIFFRACTION4A183 - 219
5X-RAY DIFFRACTION5A220 - 239
6X-RAY DIFFRACTION6A240 - 248
7X-RAY DIFFRACTION7A249 - 284
8X-RAY DIFFRACTION8A285 - 328
9X-RAY DIFFRACTION9A329 - 372

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