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- PDB-6u8z: Crystal Structure of Catalytic Domain of Human Phospholipase D1 -

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Basic information

Entry
Database: PDB / ID: 6u8z
TitleCrystal Structure of Catalytic Domain of Human Phospholipase D1
ComponentsPhospholipase D1,Phospholipase D1
KeywordsHYDROLASE / Phospholipase D1 / PLD / phosphohistidine / PIP2 binding
Function / homology
Function and homology information


Synthesis of PG / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / phospholipase D / phospholipid catabolic process / cholinergic synapse / phospholipase D activity / regulation of vesicle-mediated transport / regulation of synaptic vesicle cycle ...Synthesis of PG / phosphatidic acid biosynthetic process / regulation of microvillus assembly / Synthesis of PA / phospholipase D / phospholipid catabolic process / cholinergic synapse / phospholipase D activity / regulation of vesicle-mediated transport / regulation of synaptic vesicle cycle / cellular response to nutrient / small GTPase-mediated signal transduction / tertiary granule membrane / CDC42 GTPase cycle / endocytic vesicle / RHOG GTPase cycle / RHOA GTPase cycle / Role of phospholipids in phagocytosis / specific granule membrane / RAC1 GTPase cycle / phosphatidylinositol binding / positive regulation of translation / chemotaxis / late endosome membrane / Ras protein signal transduction / endosome / apical plasma membrane / lysosomal membrane / Golgi membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Phospholipase D, eukaryotic type / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. ...Phospholipase D, eukaryotic type / Phospholipase D family / Phospholipase D Active site motif / Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / PH domain / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
PHOSPHITE ION / Phospholipase D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.799 Å
AuthorsBowling, F.Z. / Airola, M.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128666 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM092714 United States
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Crystal structure of human PLD1 provides insight into activation by PI(4,5)P2and RhoA.
Authors: Bowling, F.Z. / Salazar, C.M. / Bell, J.A. / Huq, T.S. / Frohman, M.A. / Airola, M.V.
History
DepositionSep 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase D1,Phospholipase D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7502
Polymers69,6711
Non-polymers791
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint3 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.209, 75.209, 239.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Phospholipase D1,Phospholipase D1 / hPLD1 / Choline phosphatase 1 / Phosphatidylcholine-hydrolyzing phospholipase D1


Mass: 69671.414 Da / Num. of mol.: 1 / Fragment: UNP residues 330-500,643-1074
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLD1 / Plasmid: pFastbac Htb / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13393, phospholipase D
#2: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 0.2 M ammonium citrate, 15% PEG3350, pH 5.3

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X17B1 / Wavelength: 0.97933 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.799→79.88 Å / Num. obs: 64302 / % possible obs: 99 % / Redundancy: 8.7 % / Biso Wilson estimate: 30.221 Å2 / Rpim(I) all: 0.053 / Rrim(I) all: 0.158 / Net I/σ(I): 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.8-1.838.60.82720731470.852.53398.1
4.88-79.968182886636110.0330.096100

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.799→54.759 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.27
RfactorNum. reflection% reflection
Rfree0.2145 1816 3.13 %
Rwork0.1738 --
obs0.1751 58064 89.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.43 Å2 / Biso mean: 49.9468 Å2 / Biso min: 19.48 Å2
Refinement stepCycle: final / Resolution: 1.799→54.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4643 0 4 474 5121
Biso mean--36.42 55.78 -
Num. residues----567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7995-1.84810.35911100.3389325869
1.8481-1.90250.36791150.3085342472
1.9025-1.96390.32041210.264369478
1.9639-2.03410.2481260.2346393582
2.0341-2.11560.28171350.2113412487
2.1156-2.21180.21781410.1912432590
2.2118-2.32850.24651360.1834447394
2.3285-2.47430.22581490.1714459095
2.4743-2.66540.20081490.166469597
2.6654-2.93360.19531530.1603474098
2.9336-3.3580.1971550.1553483699
3.358-4.23050.18621600.13864938100
4.2305-54.7590.20051660.1725216100
Refinement TLS params.Method: refined / Origin x: 32.897 Å / Origin y: 70.85 Å / Origin z: 103.093 Å
111213212223313233
T0.3704 Å2-0.0799 Å2-0.0042 Å2-0.1997 Å2-0.0248 Å2--0.267 Å2
L1.2622 °2-0.3152 °20.976 °2-0.6667 °20.0688 °2--3.9283 °2
S-0.1138 Å °-0.3384 Å °0.0485 Å °-0.1683 Å °0.1334 Å °0.0037 Å °-0.6729 Å °-0.1823 Å °-0.0405 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 336:1074 OR RESID 1075:1274 ) )A336 - 1074
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 336:1074 OR RESID 1075:1274 ) )A1075 - 1274

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