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- PDB-7e0v: GDPD from Pyrococcus furiosus DSM 3638 -

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Basic information

Entry
Database: PDB / ID: 7e0v
TitleGDPD from Pyrococcus furiosus DSM 3638
ComponentsGlycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / Glycerophosphate phosphodiesterase / Hydrolysis / glycerophosphorylcholine / lysophosphorylcholine
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding / Glycerophosphodiester phosphodiesterase
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWang, Y.H. / Wang, J. / Wang, F.H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725022 China
National Natural Science Foundation of China (NSFC)31972014 China
CitationJournal: To Be Published
Title: Crystal structure of Bomgl, a monoacylglycerol lipase from marine Bacillus
Authors: Wang, Y.H. / Wang, J. / Wang, F.H.
History
DepositionJan 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerophosphodiester phosphodiesterase
C: Glycerophosphodiester phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)58,8362
Polymers58,8362
Non-polymers00
Water7,476415
1
A: Glycerophosphodiester phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)29,4181
Polymers29,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Glycerophosphodiester phosphodiesterase


Theoretical massNumber of molelcules
Total (without water)29,4181
Polymers29,4181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.330, 45.870, 96.660
Angle α, β, γ (deg.)90.000, 109.144, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycerophosphodiester phosphodiesterase


Mass: 29418.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF2003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZI9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M Hepes (pH 7.5), 25% w/v PEG3350, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97921 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.65→66.44 Å / Num. obs: 68423 / % possible obs: 97.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 24.43 Å2 / CC1/2: 0.997 / Net I/σ(I): 13.1
Reflection shellResolution: 1.65→1.69 Å / Num. unique obs: 4817 / CC1/2: 0.654

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OEC

4oec


Resolution: 1.65→66.44 Å / SU ML: 0.1458 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.7406
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1921 2000 2.93 %
Rwork0.1573 66363 -
obs0.1583 68363 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.8 Å2
Refinement stepCycle: LAST / Resolution: 1.65→66.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 0 415 4481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01674130
X-RAY DIFFRACTIONf_angle_d1.42965571
X-RAY DIFFRACTIONf_chiral_restr0.0872638
X-RAY DIFFRACTIONf_plane_restr0.0167705
X-RAY DIFFRACTIONf_dihedral_angle_d5.8779546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.25641320.23254500X-RAY DIFFRACTION93.26
1.69-1.740.22141430.20284619X-RAY DIFFRACTION95.35
1.74-1.790.20971360.1834491X-RAY DIFFRACTION92.37
1.79-1.850.22041340.16944726X-RAY DIFFRACTION96.6
1.85-1.910.19151500.16054723X-RAY DIFFRACTION97.36
1.91-1.990.21781410.15414728X-RAY DIFFRACTION97.42
1.99-2.080.18021490.1474741X-RAY DIFFRACTION97.68
2.08-2.190.16611450.14544781X-RAY DIFFRACTION98.01
2.19-2.330.18341390.14714780X-RAY DIFFRACTION97.85
2.33-2.510.17931440.14934765X-RAY DIFFRACTION98.14
2.51-2.760.18641430.15624842X-RAY DIFFRACTION98.5
2.76-3.160.21021510.16144831X-RAY DIFFRACTION98.67
3.16-3.980.1891480.15564883X-RAY DIFFRACTION98.57
3.98-66.440.18671450.15514953X-RAY DIFFRACTION97.53
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)
11.4760085168-0.3013500073840.2486630124131.45431745509-0.03444144910261.785345398960.02666528592910.024520957834-0.04577222232160.06345865431540.0192478190623-0.1508868731430.1448045036230.15111660014-0.04767839373810.197667064910.0249695354605-0.001974805273980.170397467661-0.01408589065490.19937896538-11.40279483254.441197966513.99328513672
21.81641518434-0.006089343189420.2882307445761.533502515690.04316079119220.910430485930.01267260391370.183373155580.0595453710643-0.146567286363-0.004386472017850.0283294525441-0.00752462788985-0.001713169658-0.02021782852340.1956985755680.002174758567280.006445898895380.1536249365490.01845625399040.138635534715-25.40482600259.57862887066-7.5391644423
31.627410224580.630433503163-0.1495519070141.98320659454-0.142745767081.70230939417-0.1482495596670.4241741691390.13611808585-0.3067074329060.2292092189220.3201526391950.170072948294-0.123306763603-0.06266388840210.240649660516-0.0717992990265-0.03858346287340.3719102412750.03252967512020.252709831825-7.31357015316-9.11473096815-50.5198072749
42.02472399410.712596850257-0.01461191001861.52777646828-0.1595512440130.9689203306370.01663566214560.07326026654290.201552057825-0.01506277452020.04521416247390.13109995018-0.0201244865221-0.049178486476-0.06217985807960.172033561880.003506922021840.01784322807170.178291347245-0.003511396302360.1838297342822.87214358278-2.48921838576-39.9893486228
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 127 )AA3 - 1271 - 125
22chain 'A' and (resid 128 through 253 )AA128 - 253126 - 251
33chain 'C' and (resid 3 through 94 )CB3 - 941 - 92
44chain 'C' and (resid 95 through 253 )CB95 - 25393 - 251

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