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- PDB-8h0d: Structure of the thermolabile hemolysin from Vibrio alginolyticus... -

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Basic information

Entry
Database: PDB / ID: 8h0d
TitleStructure of the thermolabile hemolysin from Vibrio alginolyticus (in complex with docosahexaenoic acid)
ComponentsSGNH/GDSL hydrolase family protein
KeywordsHYDROLASE / Vibrio / phospholipase / SGNH hydrolase / GDSL lipase / transferase / thermolabile hemolysin
Function / homology
Function and homology information


lipase activity / lipid metabolic process / metal ion binding
Similarity search - Function
: / Lipase, GDSL, active site / Lipolytic enzymes "G-D-S-L" family, serine active site. / GDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID / SGNH/GDSL hydrolase family protein
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMa, Q. / Wang, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Catalytic site flexibility facilitates the substrate and catalytic promiscuity of Vibrio dual lipase/transferase.
Authors: Wang, C. / Liu, C. / Zhu, X. / Peng, Q. / Ma, Q.
History
DepositionSep 28, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SGNH/GDSL hydrolase family protein
B: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5136
Polymers96,7572
Non-polymers7554
Water2,774154
1
A: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7072
Polymers48,3791
Non-polymers3281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8064
Polymers48,3791
Non-polymers4273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.671, 72.130, 83.489
Angle α, β, γ (deg.)90.000, 101.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SGNH/GDSL hydrolase family protein / thermolabile hemolysin


Mass: 48378.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: F0254_14065 / Plasmid: pETM13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A7Y4B3E8
#2: Chemical ChemComp-HXA / DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID


Mass: 328.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11NO3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 Å3/Da / Density % sol: 38.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystal of ValTLH in complex with docosahexaenoic acid was grown in a drop containing 1.0 ul of protein solution (6 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 300mM ...Details: The crystal of ValTLH in complex with docosahexaenoic acid was grown in a drop containing 1.0 ul of protein solution (6 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 300mM NDSB201 with 1.25 mM docosahexaenoic acid) and 1.0 ul of reservoir solution (25% polyethylene glycol 20000, 0.15 M magnesium formate).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.008→81.779 Å / Num. obs: 51148 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Rsym value: 0.076 / Net I/σ(I): 14.8
Reflection shellResolution: 2.008→2.014 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 479 / CC1/2: 0.865 / Rpim(I) all: 0.365 / Rrim(I) all: 0.927 / Rsym value: 0.85

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.27data extraction
XDSJan 10, 2022, built on 20220220data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JKZ

6jkz


Resolution: 2.01→81.779 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.161
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2527 4.96 %RANDOM
Rwork0.191 ---
obs0.193 50957 99.9 %-
Displacement parametersBiso max: 121.83 Å2 / Biso mean: 47.97 Å2 / Biso min: 23.35 Å2
Baniso -1Baniso -2Baniso -3
1-8.0406 Å20 Å20.2934 Å2
2---10.9844 Å20 Å2
3---2.9437 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.01→81.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6242 0 51 154 6447
Biso mean--65.88 39.83 -
Num. residues----777
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2166SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes185HARMONIC2
X-RAY DIFFRACTIONt_gen_planes950HARMONIC5
X-RAY DIFFRACTIONt_it6471HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion830SEMIHARMONIC5
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_contact7614SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6471HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8798HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.25
X-RAY DIFFRACTIONt_other_torsion18.69
LS refinement shellResolution: 2.01→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 174 4.64 %
Rwork0.215 3580 -
all0.216 3754 -
obs--99.73 %
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)
11.8182-0.22340.37451.3429-0.74621.6522-0.26150.04610.0410.35650.1423-0.085-0.18740.04190.1193-0.28780.0309-0.0426-0.3336-0.0684-0.3631-3.5035-2.6681-14.3947
21.70520.47090.09870.8482-0.29712.11130.0517-0.1864-0.23080.1657-0.1114-0.1273-0.1431-0.1610.0597-0.39780.0206-0.0443-0.2462-0.0023-0.3563-23.3855-32.9863-25.874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|29 - A|418 }A29 - 418
2X-RAY DIFFRACTION2{ B|30 - B|416 }B30 - 416

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