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- PDB-6jl2: Crystal structure of VvPlpA G389N from Vibrio vulnificus -

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Basic information

Entry
Database: PDB / ID: 6jl2
TitleCrystal structure of VvPlpA G389N 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 / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / Thermolabile hemolysin
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermolabile hemolysin
B: Thermolabile hemolysin
C: Thermolabile hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,81613
Polymers144,5603
Non-polymers2,25610
Water8,431468
1
A: Thermolabile hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0735
Polymers48,1871
Non-polymers8864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thermolabile hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8714
Polymers48,1871
Non-polymers6853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Thermolabile hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8714
Polymers48,1871
Non-polymers6853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.946, 64.551, 160.649
Angle α, β, γ (deg.)90.00, 116.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thermolabile hemolysin


Mass: 48186.605 Da / Num. of mol.: 3 / Mutation: G389N
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: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H11NO3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4 mg/ml in 10 mM HEPES, 150 mM NaCl, pH 7.5 was mixed with the reservoir solution (200 mM potassium sodium tartrate tetrahydrate, 180 mM NDSB-201, 14% polyethylene glycol 1500, and 5% 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: 2.298→83.68 Å / Num. obs: 63445 / % possible obs: 91.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.41 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Rsym value: 0.054 / Net I/σ(I): 21.8
Reflection shellResolution: 2.298→2.337 Å / Mean I/σ(I) obs: 5.9 / Num. unique obs: 2593 / CC1/2: 0.998 / Rpim(I) all: 0.095 / Rrim(I) all: 0.229 / Rsym value: 0.208 / % possible all: 76.2

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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: 2.3→46 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.916 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.274 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3159 4.99 %RANDOM
Rwork0.174 ---
obs0.175 63327 92 %-
Displacement parametersBiso mean: 42.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.5195 Å20 Å2-8.4921 Å2
2--10.2175 Å20 Å2
3----7.698 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 2.3→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9505 0 148 468 10121
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019945HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9913528HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3286SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes267HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1463HARMONIC5
X-RAY DIFFRACTIONt_it9945HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.05
X-RAY DIFFRACTIONt_other_torsion18.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1285SEMIHARMONIC5
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_contact11650SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 239 5.92 %
Rwork0.179 3799 -
all0.181 4038 -
obs--80.44 %
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)
10.45240.16430.1340.69040.04170.8014-0.0179-0.01540.02980.02620.04020.0368-0.0762-0.0869-0.0223-0.0810.02290.0377-0.05570.0136-0.0139160.792725.741317.6513
22.2426-0.1617-0.65760.7651-0.02020.8633-0.1615-0.1712-0.21280.05690.0313-0.08780.14440.14840.1302-0.12890.0437-0.0052-0.09660.014-0.0686207.633322.777324.7969
30.6749-0.4566-0.07081.97470.39191.041-0.1025-0.13180.03370.38150.1491-0.12240.00530.1536-0.0465-0.04290.0158-0.013-0.0773-0.018-0.1568183.035454.502351.0711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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