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- PDB-7e0m: Crystal structure of phospholipase D -

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Basic information

Entry
Database: PDB / ID: 7e0m
TitleCrystal structure of phospholipase D
ComponentsPhospholipase
KeywordsHYDROLASE / phospholipase D / LIPID BINDING PROTEIN
Function / homology
Function and homology information


phosphorus metabolic process / catalytic activity
Similarity search - Function
: / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia plymuthica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.79 Å
AuthorsWang, F.H.
CitationJournal: Int J Mol Sci / Year: 2021
Title: Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket.
Authors: Wang, F. / Liu, S. / Mao, X. / Cui, R. / Yang, B. / Wang, Y.
History
DepositionJan 28, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase
B: Phospholipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6853
Polymers87,5892
Non-polymers961
Water14,286793
1
A: Phospholipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8912
Polymers43,7951
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area15660 Å2
MethodPISA
2
B: Phospholipase


Theoretical massNumber of molelcules
Total (without water)43,7951
Polymers43,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.780, 97.570, 117.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Phospholipase


Mass: 43794.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia plymuthica (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: S4YJ13
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 793 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.2 M Diammonium hydrogen phosphate, 0.1M imidazole/HCl pH7.8, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.79→78.81 Å / Num. obs: 82957 / % possible obs: 99 % / Redundancy: 12.2 % / Biso Wilson estimate: 25.38 Å2 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.042 / Net I/σ(I): 14.3
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 3 / Num. unique obs: 5319 / CC1/2: 0.685 / Rpim(I) all: 0.393 / Χ2: 0.83 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→23.88 Å / SU ML: 0.1804 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1848 4150 5 %
Rwork0.1695 78807 -
obs0.1703 82957 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.06 Å2
Refinement stepCycle: LAST / Resolution: 1.79→23.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6096 0 5 793 6894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01126261
X-RAY DIFFRACTIONf_angle_d1.46878537
X-RAY DIFFRACTIONf_chiral_restr0.0781943
X-RAY DIFFRACTIONf_plane_restr0.01041112
X-RAY DIFFRACTIONf_dihedral_angle_d16.39422309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.810.37121070.30291957X-RAY DIFFRACTION73.98
1.81-1.830.29421190.2742093X-RAY DIFFRACTION78.02
1.83-1.850.2821090.24442291X-RAY DIFFRACTION86.05
1.85-1.880.26311230.2262532X-RAY DIFFRACTION93.62
1.88-1.90.2651500.22212531X-RAY DIFFRACTION95.51
1.9-1.930.25631580.20712573X-RAY DIFFRACTION96.64
1.93-1.960.2111410.19172628X-RAY DIFFRACTION98.05
1.96-1.980.23391340.18842626X-RAY DIFFRACTION98.71
1.98-2.020.20011270.1862697X-RAY DIFFRACTION99.02
2.02-2.050.21291260.17612646X-RAY DIFFRACTION99.04
2.05-2.080.20871300.18012681X-RAY DIFFRACTION99.19
2.08-2.120.19631280.17462660X-RAY DIFFRACTION99.04
2.12-2.160.20621430.17712674X-RAY DIFFRACTION99.19
2.16-2.210.21821320.17072680X-RAY DIFFRACTION99.19
2.21-2.250.20681420.16972662X-RAY DIFFRACTION99.4
2.25-2.310.18791450.16532681X-RAY DIFFRACTION99.54
2.31-2.370.21821360.16722683X-RAY DIFFRACTION99.61
2.37-2.430.18841250.16892694X-RAY DIFFRACTION99.61
2.43-2.50.20931380.18032696X-RAY DIFFRACTION99.47
2.5-2.580.21741440.17572685X-RAY DIFFRACTION99.72
2.58-2.670.18441750.172666X-RAY DIFFRACTION99.58
2.67-2.780.18881490.17082702X-RAY DIFFRACTION99.86
2.78-2.910.19191590.17382689X-RAY DIFFRACTION99.86
2.91-3.060.19571340.17182746X-RAY DIFFRACTION99.86
3.06-3.250.18731310.16592732X-RAY DIFFRACTION99.93
3.25-3.50.17761500.162719X-RAY DIFFRACTION99.83
3.5-3.850.14971560.15132722X-RAY DIFFRACTION99.83
3.85-4.410.1521550.14332762X-RAY DIFFRACTION99.86
4.41-5.540.14941520.14792786X-RAY DIFFRACTION99.97
5.54-23.880.15931320.17712913X-RAY DIFFRACTION99.19

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