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- PDB-6v0t: Crystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydro... -

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Basic information

Entry
Database: PDB / ID: 6v0t
TitleCrystal Structure of Catalytic Subunit of Bovine Pyruvate Dehydrogenase Phosphatase 1 - Catalytic Domain
Components[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial
KeywordsHYDROLASE / TRANSFERASE / Pyruvate Dehydrogenase Phosphatase / pyruvate dehydrogenase
Function / homology
Function and homology information


[pyruvate dehydrogenase (lipoamide)] phosphatase regulator activity / [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase / Regulation of pyruvate dehydrogenase (PDH) complex / [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity / dephosphorylation / calcium ion binding / magnesium ion binding / mitochondrion
Similarity search - Function
PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily ...PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsGuo, Y. / Qiu, W. / Ernst, S.R. / Carroll, D.W. / Hackert, M.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Robert A. Welch FoundationF-1219 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1GM132329-01 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of the catalytic subunit of bovine pyruvate dehydrogenase phosphatase.
Authors: Guo, Y. / Qiu, W. / Roche, T.E. / Hackert, M.L.
History
DepositionNov 19, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionDec 18, 2019ID: 3N3C
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1488
Polymers52,6811
Non-polymers4677
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Two crystal structures from two different species at different crystallization condition show similar interaction.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.339, 75.339, 173.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-503-

SO4

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Components

#1: Protein [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial / PDP 1 / Protein phosphatase 2C / Pyruvate dehydrogenase phosphatase catalytic subunit 1 / PDPC 1


Mass: 52681.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: P35816, [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: The protein solution was 20mg/mL in 10 mM Tris-HCl, pH 7.3, 50 mM NaCl, 1mM MnSO4, 2mM DTT, and 1mM benzamide. The well solution (mixed 1:1) contained 0.10M HEPES, pH 7.5 and 20% Jeffamine M- ...Details: The protein solution was 20mg/mL in 10 mM Tris-HCl, pH 7.3, 50 mM NaCl, 1mM MnSO4, 2mM DTT, and 1mM benzamide. The well solution (mixed 1:1) contained 0.10M HEPES, pH 7.5 and 20% Jeffamine M-600., Hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→52.117 Å / Num. obs: 33626 / % possible obs: 96 % / Redundancy: 4 % / Rsym value: 0.085 / Net I/σ(I): 35.3
Reflection shellResolution: 2.1→2.155 Å / Num. unique obs: 2014 / Rsym value: 0.33

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
PHENIX1.16-3549refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A6Q

1a6q


Resolution: 2.1→52.117 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.34
Details: Refinement was performed with Phenix Version 1.16-3549. Refinement strategy: XYZ (reciprocal-space, XYZ (real space, occupancies. Targets and Weighting, Optimize X-ray/Stereochemnistry ...Details: Refinement was performed with Phenix Version 1.16-3549. Refinement strategy: XYZ (reciprocal-space, XYZ (real space, occupancies. Targets and Weighting, Optimize X-ray/Stereochemnistry weight. Use secondary structure.
RfactorNum. reflection% reflection
Rfree0.2466 2784 8.36 %
Rwork0.2186 --
obs0.221 33298 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.03 Å2 / Biso mean: 45.2942 Å2 / Biso min: 21.17 Å2
Refinement stepCycle: final / Resolution: 2.1→52.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 15 226 3287
Biso mean--42.84 46.29 -
Num. residues----402
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.13620.30231020.2683121781
2.1362-2.17510.32741200.2759133586
2.1751-2.21690.30681250.2669143492
2.2169-2.26220.33121190.2886150599
2.2622-2.31130.28361450.24261524100
2.3113-2.36510.28521420.23191568100
2.3651-2.42430.28321370.24331534100
2.4243-2.48980.2881450.2371523100
2.4898-2.56310.28871490.2291539100
2.5631-2.64580.27811620.23381513100
2.6458-2.74040.26951450.23781551100
2.7404-2.85010.2731450.22361558100
2.8501-2.97980.26751570.21541535100
2.9798-3.13680.24371260.22361587100
3.1368-3.33330.23431190.21221573100
3.3333-3.59070.23131490.21561560100
3.5907-3.95190.2441430.19821595100
3.9519-4.52350.20641390.17531581100
4.5235-5.6980.1961580.18881605100
5.698-52.1170.2541570.2531167798

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