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- PDB-8h0b: Structure of the thermolabile hemolysin from Vibrio alginolyticus... -

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Basic information

Entry
Database: PDB / ID: 8h0b
TitleStructure of the thermolabile hemolysin from Vibrio alginolyticus (in complex with oleic 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 / extracellular region / 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
OLEIC ACID / SGNH/GDSL hydrolase family protein
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.931 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

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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)97,3035
Polymers96,7572
Non-polymers5453
Water3,621201
1
A: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8993
Polymers48,3791
Non-polymers5212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4032
Polymers48,3791
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.813, 71.871, 83.101
Angle α, β, γ (deg.)90.000, 101.460, 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-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#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.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The crystal of ValTLH in complex with oleic acid was grown in a drop containing 1.0 ul of protein solution (5 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 300 mM NDSB201 ...Details: The crystal of ValTLH in complex with oleic acid was grown in a drop containing 1.0 ul of protein solution (5 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 300 mM NDSB201 with 1 mM oleoyl coenzyme A lithium salt) and 1.0 ul of reservoir solution (22% polyethylene glycol 3350, 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, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.931→56.301 Å / Num. obs: 57066 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Rsym value: 0.047 / Net I/σ(I): 20.2
Reflection shellResolution: 1.931→1.964 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2812 / CC1/2: 0.915 / Rpim(I) all: 0.244 / Rrim(I) all: 0.645 / Rsym value: 0.596 / % possible all: 100

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Processing

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

6jkz


Resolution: 1.931→56.3 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.165 / SU Rfree Blow DPI: 0.14 / SU Rfree Cruickshank DPI: 0.143
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2779 4.87 %RANDOM
Rwork0.195 ---
obs0.196 57065 99.7 %-
Displacement parametersBiso max: 122.69 Å2 / Biso mean: 44.87 Å2 / Biso min: 23.45 Å2
Baniso -1Baniso -2Baniso -3
1-5.4026 Å20 Å23.4408 Å2
2---8.0495 Å20 Å2
3---2.647 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.931→56.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6188 0 37 201 6426
Biso mean--53.21 40.72 -
Num. residues----771
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2142SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes919HARMONIC5
X-RAY DIFFRACTIONt_it6392HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion822SEMIHARMONIC5
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_contact7606SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6392HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8685HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion18.69
LS refinement shellResolution: 1.931→1.98 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.249 196 4.77 %
Rwork0.23 3915 -
obs--98.2 %
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)
10.85450.48840.1242.2328-0.4860.9239-0.07670.07030.03180.53150.1049-0.0657-0.11050.0493-0.0283-0.21270.0422-0.0351-0.2965-0.0329-0.3666-3.3818-2.575-14.2756
20.82830.4238-0.1521.0454-0.38071.17960.05250.0141-0.25990.3063-0.1509-0.2095-0.1167-0.06040.0984-0.27530.0004-0.0976-0.2694-0.0309-0.2327-23.0655-32.5029-25.8867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|28 - A|416 }A28 - 416
2X-RAY DIFFRACTION2{ B|31 - B|416 }B31 - 416

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