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- PDB-9j3f: The structure of phospholipase TleB -

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Basic information

Entry
Database: PDB / ID: 9j3f
TitleThe structure of phospholipase TleB
ComponentsTle1 phospholipase domain-containing protein
KeywordsTOXIN / Hydrolyzed phospholipid
Function / homologyDomain of unknown function DUF2235 / T6SS, Phospholipase effector Tle1-like, catalytic domain / T6SS Phospholipase effector Tle1-like catalytic domain-containing protein
Function and homology information
Biological speciesXanthomonas oryzae pv. oryzae PXO99A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32030001 China
CitationJournal: To Be Published
Title: The structure of phospholipase TleB
Authors: Tan, Z.
History
DepositionAug 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tle1 phospholipase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3982
Polymers86,3051
Non-polymers921
Water9,260514
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area29150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.640, 70.366, 78.775
Angle α, β, γ (deg.)90.00, 99.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tle1 phospholipase domain-containing protein


Mass: 86305.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae PXO99A (bacteria)
Gene: PXO_02034
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0K0GNK3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M bis-tris pH 6.8, 23% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→46.65 Å / Num. obs: 56744 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.078 / Rrim(I) all: 0.203 / Net I/σ(I): 10.2 / Num. measured all: 379327
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.718 / Num. measured all: 24544 / Num. unique obs: 3626 / CC1/2: 0.451 / Rpim(I) all: 0.711 / Rrim(I) all: 1.862 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.65 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1966 2000 3.53 %
Rwork0.1676 --
obs0.1686 56711 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 6 514 5883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085483
X-RAY DIFFRACTIONf_angle_d0.9887420
X-RAY DIFFRACTIONf_dihedral_angle_d3.1713294
X-RAY DIFFRACTIONf_chiral_restr0.052779
X-RAY DIFFRACTIONf_plane_restr0.006986
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94760.34861400.33883853X-RAY DIFFRACTION100
1.9476-2.00020.28171430.27833881X-RAY DIFFRACTION100
2.0002-2.05910.27941430.22373911X-RAY DIFFRACTION100
2.0591-2.12550.20931410.19183878X-RAY DIFFRACTION100
2.1255-2.20150.23981430.1873907X-RAY DIFFRACTION100
2.2015-2.28970.22621420.18513870X-RAY DIFFRACTION100
2.2897-2.39390.2361440.18033927X-RAY DIFFRACTION100
2.3939-2.52010.22641410.16573891X-RAY DIFFRACTION100
2.5201-2.67790.20461430.16653906X-RAY DIFFRACTION100
2.6779-2.88470.2011430.16133907X-RAY DIFFRACTION100
2.8847-3.17490.18861430.16163922X-RAY DIFFRACTION100
3.1749-3.63420.16161440.14473908X-RAY DIFFRACTION100
3.6342-4.5780.15821440.13123956X-RAY DIFFRACTION100
4.578-46.650.15961460.15613994X-RAY DIFFRACTION99
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)
10.1441-0.1405-0.09190.42430.22190.35360.0176-0.02260.00470.01890.054-0.0422-0.02290.0326-00.07140.0005-0.00120.0847-0.01170.0803-18.5273.101-10.92
20.2901-0.1664-0.05120.35270.11750.29170.02440.0271-0.06370.0122-0.01240.0567-0.0308-0.019700.09180.012-0.00560.092-0.01620.117-31.796-20.839-33.708
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 35:450 )A35 - 450
2X-RAY DIFFRACTION2( CHAIN A AND RESID 451:681 )A451 - 681

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