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- PDB-7lhk: High-Resolution Crystal Structure of a Lipin/Pah Phosphatidic Aci... -

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Basic information

Entry
Database: PDB / ID: 7lhk
TitleHigh-Resolution Crystal Structure of a Lipin/Pah Phosphatidic Acid Phosphatase
ComponentsNuclear elongation and deformation protein
KeywordsHYDROLASE / lipin / phosphohydrolase / phosphatidic acid phosphatase / haloalkanoic acid dehalogenase
Function / homology
Function and homology information


Lipin, N-terminal / Lipin/Ned1/Smp2 (LNS2) / LIPIN family / LNS2/PITP / lipin, N-terminal conserved region / LNS2 (Lipin/Ned1/Smp2) / LNS2 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
CACODYLATE ION / Nuclear elongation and deformation protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKhayyo, V.I. / Airola, M.V.
Funding support United States, 3items
OrganizationGrant numberCountry
American Heart Association19PRE34450192 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128666 United States
American Heart Association17SDG33410860 United States
CitationJournal: To be published
Title: High-resolution structure of phosphatidic acid phosphohydrolase from Tetrahymena thermophila
Authors: Khayyo, V.I. / Airola, M.V.
History
DepositionJan 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Nuclear elongation and deformation protein
B: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7904
Polymers71,5162
Non-polymers2742
Water10,377576
1
A: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,7581
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8952
Polymers35,7581
Non-polymers1371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.410, 171.626, 62.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-535-

HOH

21A-831-

HOH

31B-918-

HOH

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Components

#1: Protein Nuclear elongation and deformation protein


Mass: 35758.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (strain SB210) (eukaryote)
Strain: SB210 / Gene: TTHERM_00215970 / Plasmid: ppSUMO
Production host: Escherichia coli BL21(DE3)-RIPL competent (bacteria)
References: UniProt: I7MFJ3
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Tt Pah2 in a ratio of 2:1 with well solution of 0.1M sodium cacodylate pH 6.5, 1 M NaCl, 10% glycerol, 30% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.95→55.25 Å / Num. obs: 720604 / % possible obs: 99.54 % / Redundancy: 12.6 % / Biso Wilson estimate: 30.57 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08466 / Rpim(I) all: 0.02437 / Rrim(I) all: 0.08818 / Net I/σ(I): 16.77
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.87 / Num. unique obs: 5410 / CC1/2: 0.907 / CC star: 0.975 / Rpim(I) all: 0.2381 / Rrim(I) all: 0.686 / % possible all: 95.83

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.6.2data scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TZY

6tzy


Resolution: 1.95→55.25 Å / SU ML: 0.1972 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.6774 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 2782 4.94 %
Rwork0.165 53567 -
obs0.1672 56349 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.45 Å2
Refinement stepCycle: LAST / Resolution: 1.95→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 0 576 5369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114935
X-RAY DIFFRACTIONf_angle_d1.09446668
X-RAY DIFFRACTIONf_chiral_restr0.0634738
X-RAY DIFFRACTIONf_plane_restr0.0069857
X-RAY DIFFRACTIONf_dihedral_angle_d2.66834205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.28721060.26362354X-RAY DIFFRACTION87.83
1.98-2.020.27261340.23522524X-RAY DIFFRACTION93.62
2.02-2.060.26071290.20722603X-RAY DIFFRACTION96.67
2.06-2.10.25931440.18962648X-RAY DIFFRACTION97.45
2.1-2.150.22921320.17432621X-RAY DIFFRACTION98.08
2.15-2.20.23371170.17142689X-RAY DIFFRACTION98.42
2.2-2.250.22671290.16872679X-RAY DIFFRACTION98.77
2.25-2.310.21921330.16012641X-RAY DIFFRACTION98.75
2.31-2.380.21861700.15542644X-RAY DIFFRACTION98.81
2.38-2.460.21531230.15142709X-RAY DIFFRACTION99.44
2.46-2.540.20221510.14992695X-RAY DIFFRACTION99.58
2.54-2.650.1981560.15572672X-RAY DIFFRACTION99.75
2.65-2.770.20761430.15352716X-RAY DIFFRACTION99.76
2.77-2.910.18771580.15262702X-RAY DIFFRACTION99.83
2.91-3.10.18631420.15372705X-RAY DIFFRACTION99.86
3.1-3.330.22731670.15712712X-RAY DIFFRACTION100
3.33-3.670.18671150.14942796X-RAY DIFFRACTION100
3.67-4.20.19271360.14392748X-RAY DIFFRACTION100
4.2-5.290.17141400.13982810X-RAY DIFFRACTION100
5.29-55.250.24561570.21322899X-RAY DIFFRACTION99.84

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