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- PDB-8h09: Structure of the thermolabile hemolysin from Vibrio alginolyticus... -

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Basic information

Entry
Database: PDB / ID: 8h09
TitleStructure of the thermolabile hemolysin from Vibrio alginolyticus (apo form)
ComponentsSGNH/GDSL hydrolase family protein
KeywordsHYDROLASE / Vibrio / phospholipase / SGNH hydrolase / GDSL lipase / transferase / 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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / DI(HYDROXYETHYL)ETHER / SGNH/GDSL hydrolase family protein
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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

Downloads & links

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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)99,33318
Polymers96,7572
Non-polymers2,57616
Water5,531307
1
A: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,70710
Polymers48,3791
Non-polymers1,3289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SGNH/GDSL hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6268
Polymers48,3791
Non-polymers1,2487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.932, 71.238, 83.645
Angle α, β, γ (deg.)90.000, 101.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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 (E. coli) / Strain (production host): Escherichia coli C43 (DE3) / References: UniProt: A0A7Y4B3E8

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Non-polymers , 5 types, 323 molecules

#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / 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.: 4 / Source method: obtained synthetically / Formula: C8H11NO3S
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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Details

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 was grown in a drop containing 1.0 ul of protein solution (10 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 200 mM NDSB201) and 1.0 ul of reservoir ...Details: The crystal of ValTLH was grown in a drop containing 1.0 ul of protein solution (10 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT, 200 mM NDSB201) and 1.0 ul of reservoir solution (0.1 M Tris pH 8.5, 20.5% polyethylene glycol 4000, 20% polyethylene glycol 400, and 0.1 M MgCl2).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97876 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97876 Å / Relative weight: 1
ReflectionResolution: 1.809→53.783 Å / Num. obs: 68600 / % possible obs: 98.8 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Rsym value: 0.08 / Net I/σ(I): 12.9
Reflection shellResolution: 1.809→1.84 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3412 / CC1/2: 0.863 / Rpim(I) all: 0.288 / Rrim(I) all: 0.767 / Rsym value: 0.709 / % possible all: 98.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
PDB_EXTRACT3.27data extraction
XDSMar 15, 2019, built on 20190315data reduction
Aimless0.5.29data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JKZ

6jkz


Resolution: 1.81→53.78 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.115
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3351 4.89 %RANDOM
Rwork0.18 ---
obs0.181 68495 98.8 %-
Displacement parametersBiso max: 112.16 Å2 / Biso mean: 36.7 Å2 / Biso min: 16.19 Å2
Baniso -1Baniso -2Baniso -3
1-3.563 Å20 Å21.514 Å2
2---8.303 Å20 Å2
3---4.74 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.81→53.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6150 0 169 307 6626
Biso mean--56.84 37.52 -
Num. residues----764
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2206SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes182HARMONIC2
X-RAY DIFFRACTIONt_gen_planes942HARMONIC5
X-RAY DIFFRACTIONt_it6484HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion818SEMIHARMONIC5
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_contact7862SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6484HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8774HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion17.15
LS refinement shellResolution: 1.81→1.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 224 4.45 %
Rwork0.197 4811 -
all0.197 5035 -
obs--98.65 %
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)
11.01460.08670.10240.5989-0.30880.9724-0.06160.034-0.0373-0.01670.07060.11240.0278-0.0015-0.009-0.0956-0.00990.0003-0.122-0.013-0.0804-2.785-5.9093-12.8564
21.3566-0.27510.76340.5325-0.2142.3469-0.0106-0.1879-0.0914-0.00310.00410.1181-0.2391-0.31730.0065-0.130.0423-0.0222-0.1507-0.0178-0.1434-24.24-36.644-27.1788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|30 - A|418 }A30 - 418
2X-RAY DIFFRACTION2{ B|31 - B|416 }B31 - 416

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