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- PDB-6jl1: Crystal structure of VvPlpA G389D from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 6jl1
TitleCrystal structure of VvPlpA G389D 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 / Thermolabile hemolysin
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 1.3Nov 22, 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
Revision 1.4Nov 13, 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


Theoretical massNumber of molelcules
Total (without water)48,1881
Polymers48,1881
Non-polymers00
Water1,820101
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)54.397, 54.397, 233.181
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: 48187.590 Da / Num. of mol.: 1 / Mutation: G389D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: CRN61_10355 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S3SYP4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 5 mg/ml in 10 mM HEPES, 150 mM NaCl, pH 7.5 was mixed with equal volume of reservoir solution (200 mM potassium sodium tartrate tetrahydrate, 180 mM NDSB-201, 8% polyethylene glycol 1500, and 20% glycerol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 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: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.288→47.103 Å / Num. obs: 19033 / % possible obs: 100 % / Redundancy: 18.6 % / Biso Wilson estimate: 51.83 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.023 / Rrim(I) all: 0.097 / Rsym value: 0.094 / Net I/σ(I): 17.3
Reflection shellResolution: 2.288→2.327 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 3 / Num. unique obs: 917 / CC1/2: 0.969 / Rpim(I) all: 0.18 / Rrim(I) all: 0.734 / Rsym value: 0.711 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JKZ

6jkz


Resolution: 2.29→47.1 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.893 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.333 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.226 / SU Rfree Cruickshank DPI: 0.224
RfactorNum. reflection% reflectionSelection details
Rfree0.235 876 4.61 %RANDOM
Rwork0.193 ---
obs0.195 18984 100 %-
Displacement parametersBiso mean: 57.55 Å2
Baniso -1Baniso -2Baniso -3
1--10.7744 Å20 Å20 Å2
2---10.7744 Å20 Å2
3---21.5488 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 2.29→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 0 101 3301
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013296HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.024492HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1076SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes476HARMONIC5
X-RAY DIFFRACTIONt_it3296HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion19.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion432SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3702SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.287 140 5.19 %
Rwork0.204 2559 -
all0.208 2699 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 20.7689 Å / Origin y: -5.2229 Å / Origin z: 20.2064 Å
111213212223313233
T-0.1026 Å2-0.0003 Å20.0063 Å2-0.0523 Å2-0.0299 Å2---0.1481 Å2
L1.1185 °20.4238 °2-0.0639 °2-0.8222 °2-0.1496 °2--1.1275 °2
S-0.0034 Å °-0.2821 Å °0.0896 Å °0.0336 Å °-0.0243 Å °0.0342 Å °-0.0637 Å °-0.0651 Å °0.0277 Å °
Refinement TLS groupSelection details: { A|* }

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