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- PDB-6tzy: Crystal Structure of a lipin/Pah Phosphatidic Acid Phosphatase -

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Basic information

Entry
Database: PDB / ID: 6tzy
TitleCrystal Structure of a lipin/Pah Phosphatidic Acid Phosphatase
ComponentsNuclear elongation and deformation protein
KeywordsHYDROLASE / Lipin / phosphatidic acid phosphatase / immunoglobulin-like / haloacid 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
Nuclear elongation and deformation protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 3 Å
AuthorsKhayyo, V.I. / Airola, M.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128666 United States
American Heart Association17SDG33410860 United States
American Heart Association19PRE34450192 United States
CitationJournal: Nat Commun / Year: 2020
Title: Crystal Structure of a lipin/Pah Phosphatidic Acid Phosphatase
Authors: Khayyo, V.I. / Hoffmann, R.M. / Wang, H. / Bell, J.A. / Burke, J.E. / Reue, K. / Airola, M.V.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear elongation and deformation protein
B: Nuclear elongation and deformation protein
C: Nuclear elongation and deformation protein
D: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,1379
Polymers146,9374
Non-polymers2005
Water1,04558
1
A: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7742
Polymers36,7341
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8143
Polymers36,7341
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7742
Polymers36,7341
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7742
Polymers36,7341
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.017, 135.126, 90.974
Angle α, β, γ (deg.)90.000, 116.190, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nuclear elongation and deformation protein


Mass: 36734.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TTHERM_00215970 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: I7MFJ3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.91 Å3/Da / Density % sol: 35.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M Ca(NO3)2, 15% PEG 8,000, 0.1M MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.66→53.23 Å / Num. obs: 33662 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.039 / Rrim(I) all: 0.103 / Net I/σ(I): 10 / Num. measured all: 235447 / Scaling rejects: 694
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.66-2.737.20.9351781724810.3960.3761.0091.8100
11.9-53.236.70.04126283920.9980.0170.04532.999.1

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.6.2data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TZZ

6tzz


Resolution: 3→52.05 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 30.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2676 1182 5.03 %
Rwork0.2366 22313 -
obs0.2382 23495 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 282.16 Å2 / Biso mean: 95.6948 Å2 / Biso min: 31.54 Å2
Refinement stepCycle: final / Resolution: 3→52.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8590 0 5 58 8653
Biso mean--114.42 60.39 -
Num. residues----1063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.0001-3.13660.35541330.29972814
3.1366-3.3020.33641230.30722783
3.302-3.50880.32711630.29412750
3.5088-3.77960.30831550.26652779
3.7796-4.15980.26291500.2352789
4.1598-4.76140.22311530.20942774
4.7614-5.99750.23491510.21292789
5.9975-52.050.26351540.2192835
Refinement TLS params.Method: refined / Origin x: 6.162 Å / Origin y: -20.539 Å / Origin z: 29.901 Å
111213212223313233
T0.3599 Å20.0874 Å2-0.0089 Å2-0.3662 Å20.0416 Å2--0.3585 Å2
L0.2188 °20.2035 °2-0.03 °2-0.1338 °20.0069 °2--0.3274 °2
S0.0457 Å °0.0068 Å °-0.0294 Å °0.0317 Å °-0.1231 Å °0.0233 Å °-0.0922 Å °0.0086 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )A21 - 321
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )A401
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )A501 - 518
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )C20 - 320
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )C401
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )C501 - 512
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )B20 - 320
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )B400 - 401
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )B501 - 518
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )D501 - 510
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )D20 - 321
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 401:401 OR RESID 501:518 ) ) OR ( CHAIN C AND ( RESID 20:320 OR RESID 401:401 OR RESID 501:512 ) ) OR ( CHAIN B AND ( RESID 20:320 OR RESID 400:401 OR RESID 501:518 ) ) OR ( CHAIN D AND ( RESID 501:510 OR RESID 20:321 OR RESID 401:401 ) )D401

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