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- PDB-7js5: Phospholipase D engineered mutant (TNYR) inactive enzyme (H168A) ... -

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Basic information

Entry
Database: PDB / ID: 7js5
TitlePhospholipase D engineered mutant (TNYR) inactive enzyme (H168A) bound to 1-inositol phosphate
ComponentsPhospholipase D
KeywordsLIPID BINDING PROTEIN / engineered mutant / pseudo-dimeric architecture / myo-inositol specificity
Function / homology
Function and homology information


phosphatidyltransferase activity / cardiolipin biosynthetic process / phospholipase D / phospholipase D activity / lipid catabolic process / extracellular region
Similarity search - Function
Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile.
Similarity search - Domain/homology
D-MYO-INOSITOL-1-PHOSPHATE / Phospholipase D
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVrielink, A. / Samantha, A.
CitationJournal: Biochem.J. / Year: 2021
Title: Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation.
Authors: Samantha, A. / Damnjanovic, J. / Iwasaki, Y. / Nakano, H. / Vrielink, A.
History
DepositionAug 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3944
Polymers53,8491
Non-polymers5453
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint7 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.127, 83.151, 99.393
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 D / Choline phosphatase


Mass: 53848.844 Da / Num. of mol.: 1 / Fragment: UNP residues 48-556 / Mutation: V107S,H168A,G186T,W187N,A211R,Y385R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q53728, phospholipase D
#2: Chemical ChemComp-IPD / D-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 15% PEG6000, 100 mM MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 2.5→48.19 Å / Num. obs: 17538 / % possible obs: 99.94 % / Redundancy: 13.6 % / Biso Wilson estimate: 42.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1744 / Net I/σ(I): 14.38
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 2.066 / Num. unique obs: 2516 / CC1/2: 0.723 / % possible all: 99.72

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZE4

2ze4


Resolution: 2.5→48.19 Å / SU ML: 0.3082 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 900 5.13 %
Rwork0.172 16631 -
obs0.1766 17531 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.02 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3688 0 34 140 3862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723801
X-RAY DIFFRACTIONf_angle_d0.93575189
X-RAY DIFFRACTIONf_chiral_restr0.0527589
X-RAY DIFFRACTIONf_plane_restr0.0053680
X-RAY DIFFRACTIONf_dihedral_angle_d14.9995538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.34131280.21432721X-RAY DIFFRACTION99.96
2.66-2.860.30861510.20872726X-RAY DIFFRACTION100
2.86-3.150.27751420.19932744X-RAY DIFFRACTION99.97
3.15-3.610.29841630.1792749X-RAY DIFFRACTION99.97
3.61-4.540.23551580.14762771X-RAY DIFFRACTION99.97
4.54-48.190.23561580.15932920X-RAY DIFFRACTION99.94

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