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- PDB-6tzz: Crystal Structure of Tetrahymena Thermophila Lipin Phosphatidic A... -

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Basic information

Entry
Database: PDB / ID: 6tzz
TitleCrystal Structure of Tetrahymena Thermophila Lipin Phosphatidic Acid Phosphatase with Magnesium
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 1.1Mar 13, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)73,6914
Polymers73,6422
Non-polymers492
Water52229
1
A: Nuclear elongation and deformation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8462
Polymers36,8211
Non-polymers241
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)36,8462
Polymers36,8211
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.410, 57.644, 84.191
Angle α, β, γ (deg.)90.000, 114.900, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 21 through 46 or resid 54...
21(chain B and (resid 21 through 154 or resid 168 through 321))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEPHEPHE(chain A and (resid 21 through 46 or resid 54...AA21 - 4622 - 47
12ASNASNGLUGLU(chain A and (resid 21 through 46 or resid 54...AA54 - 8555 - 86
13GLNGLNGLNGLN(chain A and (resid 21 through 46 or resid 54...AA93 - 22694 - 227
14GLUGLUPROPRO(chain A and (resid 21 through 46 or resid 54...AA242 - 321243 - 322
21PHEPHESERSER(chain B and (resid 21 through 154 or resid 168 through 321))BB21 - 15422 - 155
22TRPTRPPROPRO(chain B and (resid 21 through 154 or resid 168 through 321))BB168 - 321169 - 322

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Components

#1: Protein Nuclear elongation and deformation protein / Lipin Phosphatidic Acid Phosphatase


Mass: 36821.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TTHERM_00215970 / Plasmid: ppSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIPL / References: UniProt: I7MFJ3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Mg(NO3)2, 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.91839 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: 0.91839 Å / Relative weight: 1
ReflectionResolution: 2.58→47.52 Å / Num. obs: 23065 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.985 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.102 / Rrim(I) all: 0.27 / Net I/σ(I): 4.4 / Num. measured all: 158812 / Scaling rejects: 72
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
2.58-2.657.11.2471212217130.4110.5051.3471.5100
11.54-47.526.70.14718982830.9820.0590.15910.998.8

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→47.492 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 34.91
RfactorNum. reflection% reflection
Rfree0.2875 760 5.19 %
Rwork0.2423 --
obs0.2447 14630 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.71 Å2 / Biso mean: 70.1488 Å2 / Biso min: 18.08 Å2
Refinement stepCycle: final / Resolution: 3→47.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 2 29 4388
Biso mean--57.65 42.34 -
Num. residues----538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1542X-RAY DIFFRACTION8.513TORSIONAL
12B1542X-RAY DIFFRACTION8.513TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3-3.23160.34071460.30272747
3.2316-3.55670.30521500.25152739
3.5567-4.07110.27621510.24132757
4.0711-5.12820.27971550.2022781
5.1282-47.4920.27661580.2542846
Refinement TLS params.Method: refined / Origin x: -22.161 Å / Origin y: 1.958 Å / Origin z: 1.164 Å
111213212223313233
T0.1509 Å2-0.011 Å2-0.0237 Å2-0.114 Å20.0473 Å2--0.4523 Å2
L0.5824 °2-0.0309 °2-0.0858 °2-0.0764 °20.2774 °2--0.3873 °2
S0.0122 Å °0.0178 Å °0.0573 Å °0.016 Å °0.0206 Å °-0.0369 Å °-0.0751 Å °0.1617 Å °0.0428 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 501:520 OR RESID 401:401 ) ) OR ( CHAIN B AND ( RESID 501:509 OR RESID 20:321 OR RESID 401:401 ) )A21 - 321
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 501:520 OR RESID 401:401 ) ) OR ( CHAIN B AND ( RESID 501:509 OR RESID 20:321 OR RESID 401:401 ) )A501 - 520
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 501:520 OR RESID 401:401 ) ) OR ( CHAIN B AND ( RESID 501:509 OR RESID 20:321 OR RESID 401:401 ) )A401
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 501:520 OR RESID 401:401 ) ) OR ( CHAIN B AND ( RESID 501:509 OR RESID 20:321 OR RESID 401:401 ) )B501 - 509
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 501:520 OR RESID 401:401 ) ) OR ( CHAIN B AND ( RESID 501:509 OR RESID 20:321 OR RESID 401:401 ) )B20 - 321
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 21:321 OR RESID 501:520 OR RESID 401:401 ) ) OR ( CHAIN B AND ( RESID 501:509 OR RESID 20:321 OR RESID 401:401 ) )B401

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