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- PDB-6bqm: Secreted serine protease VesC from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 6bqm
TitleSecreted serine protease VesC from Vibrio cholerae
Componentsserine protease VesC
KeywordsHYDROLASE / VC1649 / trypsin-like domain / Ig-like domain / CBM domain
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / membrane
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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain ...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 family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold
Similarity search - Domain/homology
Trypsin / Trypsin, putative
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPark, Y.J. / Korotkov, K.V. / Delarosa, J.R. / Turley, S. / DiMaio, F. / Hol, W.G.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI034501 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Msphere / Year: 2020
Title: Suppressor Mutations in Type II Secretion Mutants of Vibrio cholerae: Inactivation of the VesC Protease.
Authors: Rule, C.S. / Park, Y.J. / Delarosa, J.R. / Turley, S. / Hol, W.G.J. / McColm, S. / Gura, C. / DiMaio, F. / Korotkov, K.V. / Sandkvist, M.
History
DepositionNov 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: serine protease VesC


Theoretical massNumber of molelcules
Total (without water)55,3531
Polymers55,3531
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.651, 83.402, 123.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein serine protease VesC


Mass: 55353.141 Da / Num. of mol.: 1 / Fragment: UNP residues 23-522 / Mutation: S225A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A1254 / Plasmid: pRSF-CT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta(DE3)
References: UniProt: A0A0H3AHB9, UniProt: Q9KRJ1*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.93 Å3/Da / Density % sol: 36.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, pH 8.5, 0.2 M calcium chloride, 0.6 M sodium chloride, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97939 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 18, 2011
Details: Flat bent collimating Rh coated mirror, toroidal focusing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.2→69.05 Å / Num. obs: 22516 / % possible obs: 100 % / Redundancy: 7.24 % / Biso Wilson estimate: 43.056 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.104 / Χ2: 0.99 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.266.9850.9692.2716140.6971.047100
2.26-2.327.3730.7723.0216070.8280.831100
2.32-2.397.3870.6293.6315420.8740.676100
2.39-2.467.3890.5234.3515330.9070.562100
2.46-2.547.4030.4544.8814290.9240.489100
2.54-2.637.3560.368614310.9630.396100
2.63-2.737.3720.2857.7213720.9650.307100
2.73-2.847.3490.2319.2613140.9820.249100
2.84-2.977.3550.1911.0912940.9850.204100
2.97-3.117.3410.1414.1312010.9930.1599.9
3.11-3.287.3310.10218.3211710.9960.11100
3.28-3.487.2310.07323.7811130.9980.079100
3.48-3.727.2660.05828.3410370.9980.063100
3.72-4.027.2420.04932.089540.9980.052100
4.02-4.47.150.04136.859140.9990.045100
4.4-4.927.1360.03940.748230.9990.042100
4.92-5.686.9730.04238.897280.9980.045100
5.68-6.966.8410.04336.76410.9980.046100
6.96-9.846.6470.03941.174960.9990.042100
9.84-69.055.7150.03644.53020.9980.03998.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSNovember 11, 2013 BUILT=20131111data reduction
XSCALENovember 11, 2013 BUILT=20131111data scaling
PHASERphasing
REFMAC5.8.0107refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 4LK4, 1UXX, 2C9A

4lk4

1uxx

2c9a


Resolution: 2.2→39.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.75 / SU ML: 0.178 / SU R Cruickshank DPI: 0.3293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 1113 4.9 %RANDOM
Rwork0.2008 ---
obs0.2024 21402 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.43 Å2 / Biso mean: 37.582 Å2 / Biso min: 16.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0 Å20 Å2
2--0.96 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 2.2→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3527 0 0 124 3651
Biso mean---33.54 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193607
X-RAY DIFFRACTIONr_bond_other_d0.0030.023285
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9344904
X-RAY DIFFRACTIONr_angle_other_deg1.07737527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2495456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31724.425174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15515546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.291519
X-RAY DIFFRACTIONr_chiral_restr0.110.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024220
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02881
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 86 -
Rwork0.273 1525 -
all-1611 -
obs--100 %
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)
12.84561.1224-0.58991.9223-0.35114.12640.0906-0.11070.14370.4932-0.01560.4515-0.2886-0.4829-0.0750.19760.04080.10470.06930.00010.125641.5312107.317847.1579
21.3108-0.0968-0.38424.0627-0.5572.1657-0.0514-0.1593-0.09150.59660.0748-0.07930.02620.0489-0.02340.1165-0.0037-0.02120.0570.00070.027750.911898.894547.4554
31.6896-0.9283-1.57714.27551.41133.6496-0.03110.2137-0.13280.2221-0.03430.36950.2377-0.52490.06550.1369-0.0232-0.0160.11030.01620.112445.198287.143243.451
40.9050.14890.292.1994-0.50812.39930.0157-0.0389-0.03660.3607-0.0424-0.1326-0.18280.20480.02670.0667-0.0075-0.02520.0448-0.00510.012854.1094105.100535.9806
51.9887-0.14980.55371.6516-0.94173.164-0.01610.14930.11840.2044-0.0527-0.2159-0.31780.33380.06880.0519-0.028-0.0090.05330.00970.049258.4484113.851826.2684
63.4544-0.5438-0.89162.59580.11712.8259-0.1846-0.2496-0.29490.1390.05820.16370.2674-0.11090.12640.03750.00420.02140.04570.01690.036234.040797.516312.4167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 110
2X-RAY DIFFRACTION2A111 - 161
3X-RAY DIFFRACTION3A162 - 229
4X-RAY DIFFRACTION4A230 - 320
5X-RAY DIFFRACTION5A321 - 377
6X-RAY DIFFRACTION6A378 - 489

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