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- PDB-6jl0: Crystal structure of VvPlpA from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 6jl0
TitleCrystal structure of VvPlpA from Vibrio vulnificus
ComponentsThermolabile hemolysin
KeywordsHYDROLASE / Vibrio / phospholipase / SGNH hydrolase
Function / homologyLipase, GDSL, active site / Lipolytic enzymes "G-D-S-L" family, serine active site. / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / lipase activity / SGNH hydrolase superfamily / lipid metabolic process / BROMIDE ION / Thermolabile hemolysin
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.073 Å
AuthorsMa, Q. / Wan, Y. / Liu, C.
Funding support China, 2items
OrganizationGrant numberCountry
Other government1000 talent program China
Chinese Academy of Sciences100 talent program China
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural analysis of aVibriophospholipase reveals an unusual Ser-His-chloride catalytic triad.
Authors: Wan, Y. / Liu, C. / Ma, Q.
History
DepositionMar 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Apr 3, 2024Group: 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermolabile hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2092
Polymers48,1301
Non-polymers801
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.865, 53.865, 232.287
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Thermolabile hemolysin


Mass: 48129.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN61_10355 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S3SYP4
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5 mg/ml protein in 10 mM HEPES, 150 mM NaBr, pH 7.5, was mixed with equal volume reservoir solution (200 mM potassium sodium tartrate tetrahydrate, 180 mM NDSB-201, 12% polyethylene glycol ...Details: 5 mg/ml protein in 10 mM HEPES, 150 mM NaBr, pH 7.5, was mixed with equal volume reservoir solution (200 mM potassium sodium tartrate tetrahydrate, 180 mM NDSB-201, 12% polyethylene glycol 1500, and 10% glycerine)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9163 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.073→45.736 Å / Num. obs: 24564 / % possible obs: 99.1 % / Redundancy: 18.2 % / CC1/2: 0.998 / Rpim(I) all: 0.019 / Rrim(I) all: 0.082 / Rsym value: 0.079 / Net I/σ(I): 20.9
Reflection shellResolution: 2.073→2.109 Å / Redundancy: 12 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 998 / CC1/2: 0.896 / Rpim(I) all: 0.185 / Rrim(I) all: 0.684 / Rsym value: 0.656 / % possible all: 86.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: our own model

Resolution: 2.073→45.735 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98
RfactorNum. reflection% reflection
Rfree0.2268 2284 5.06 %
Rwork0.1907 --
obs0.1926 24562 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.073→45.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 1 117 3309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143291
X-RAY DIFFRACTIONf_angle_d1.3014486
X-RAY DIFFRACTIONf_dihedral_angle_d12.4651895
X-RAY DIFFRACTIONf_chiral_restr0.084475
X-RAY DIFFRACTIONf_plane_restr0.011576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.073-2.1180.32091230.28322222X-RAY DIFFRACTION84
2.118-2.16730.29681390.24982714X-RAY DIFFRACTION98
2.1673-2.22150.26071240.22062685X-RAY DIFFRACTION100
2.2215-2.28160.25191400.23392691X-RAY DIFFRACTION100
2.2816-2.34870.31081900.22952718X-RAY DIFFRACTION100
2.3487-2.42450.32961220.22042681X-RAY DIFFRACTION100
2.4245-2.51120.29911180.21742708X-RAY DIFFRACTION100
2.5112-2.61170.23511480.2062726X-RAY DIFFRACTION100
2.6117-2.73050.23091240.21112773X-RAY DIFFRACTION100
2.7305-2.87450.26151340.21522706X-RAY DIFFRACTION100
2.8745-3.05450.23561360.2122706X-RAY DIFFRACTION100
3.0545-3.29030.22541680.1982682X-RAY DIFFRACTION100
3.2903-3.62130.21451630.18752717X-RAY DIFFRACTION100
3.6213-4.1450.20171600.16362709X-RAY DIFFRACTION100
4.145-5.22110.1821480.15332699X-RAY DIFFRACTION100
5.2211-45.74640.21481470.18172709X-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)
13.0648-0.4535-0.7842.2901-0.26526.1271-0.221-0.033-0.2591-0.07670.07820.53730.0823-0.27390.34340.4619-0.1198-0.04550.58350.00720.5245-4.5612-8.560613.2862
22.42861.09910.01051.00810.02531.6046-0.06260.10240.1167-0.19330.05870.00740.0436-0.0751-0.00240.4763-0.1379-0.04270.43070.02710.371116.6119-0.88924.5703
31.28971.0545-0.27491.2828-0.75550.7182-0-0.16340.0877-0.0059-0.02960.0251-0.00660.01260.02580.428-0.1471-0.0090.466-0.02550.395220.5002-3.590118.0923
40.8961-0.0392-0.68370.066-0.24251.67670.4604-0.25280.40710.597-0.15290.32010.098-0.2998-0.15170.6352-0.08030.02240.8110.00730.785613.04927.087929.2077
52.0902-0.11290.77531.9011-0.73142.1508-0.0335-0.39360.11150.0542-0.01190.2378-0.0964-0.11440.07620.3489-0.19720.02030.5403-0.02450.320512.1808-11.132127.7793
60.5980.56080.26362.21250.18561.26730.2307-0.47990.02480.0311-0.3569-0.0987-0.09310.01090.11370.4662-0.3036-0.0370.78280.07430.409927.0377-10.266736.3741
71.2910.91360.10931.49770.25691.12630.1197-0.18830.0977-0.0014-0.0964-0.2151-0.15850.2723-0.0120.3706-0.1552-0.00380.5120.02370.360834.154-3.618322.6598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 24:41)
2X-RAY DIFFRACTION2(chain A and resid 42:138)
3X-RAY DIFFRACTION3(chain A and resid 139:206)
4X-RAY DIFFRACTION4(chain A and resid 207:214)
5X-RAY DIFFRACTION5(chain A and resid 215:281)
6X-RAY DIFFRACTION6(chain A and resid 282:342)
7X-RAY DIFFRACTION7(chain A and resid 343:421)

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