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- PDB-2pnq: Crystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1) -

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Basic information

Entry
Database: PDB / ID: 2pnq
TitleCrystal structure of pyruvate dehydrogenase phosphatase 1 (PDP1)
Components[Pyruvate dehydrogenase [lipoamide]]-phosphatase 1
KeywordsHYDROLASE / pyruvate dehydrogenase phosphatase 1 / catalytic subunit / PDP1c
Function / homology
Function and homology information


[pyruvate dehydrogenase (acetyl-transferring)]-phosphatase / positive regulation of pyruvate dehydrogenase activity / Regulation of pyruvate dehydrogenase (PDH) complex / protein serine/threonine phosphatase activity => GO:0004722 / [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity / peptidyl-threonine dephosphorylation / protein serine/threonine phosphatase activity / positive regulation of catalytic activity / protein dephosphorylation / mitochondrial matrix ...[pyruvate dehydrogenase (acetyl-transferring)]-phosphatase / positive regulation of pyruvate dehydrogenase activity / Regulation of pyruvate dehydrogenase (PDH) complex / protein serine/threonine phosphatase activity => GO:0004722 / [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity / peptidyl-threonine dephosphorylation / protein serine/threonine phosphatase activity / positive regulation of catalytic activity / protein dephosphorylation / mitochondrial matrix / calcium ion binding / protein-containing complex 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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.81 Å
AuthorsVassylyev, D.G. / Symersky, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of pyruvate dehydrogenase phosphatase 1 and its functional implications.
Authors: Vassylyev, D.G. / Symersky, J.
History
DepositionApr 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: [Pyruvate dehydrogenase [lipoamide]]-phosphatase 1
B: [Pyruvate dehydrogenase [lipoamide]]-phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4626
Polymers105,3642
Non-polymers974
Water8,629479
1
A: [Pyruvate dehydrogenase [lipoamide]]-phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7313
Polymers52,6821
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: [Pyruvate dehydrogenase [lipoamide]]-phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7313
Polymers52,6821
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.318, 72.220, 96.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe bilogical assembly is a monomer

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Components

#1: Protein [Pyruvate dehydrogenase [lipoamide]]-phosphatase 1 / PDP 1 / Pyruvate dehydrogenase phosphatase / catalytic subunit 1 / PDPC 1 / Protein phosphatase 2C


Mass: 52682.223 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pdp1, Ppm2c / Plasmid: pPDP1c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: O88483, [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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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: 2.150221 Å3/Da / Density % sol: 42.79657 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: Protein solution: protein 10mg/ml, 50 mM Tris pH 8.0, 5 mM MgCl2, 50 mM KCl, 0.1 mM EDTA Precipitant solution: 30% ethylene glycol, 0.1 M MES pH 6.0, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2006
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→30 Å / Num. all: 64759 / Num. obs: 64759 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 40.3 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 15
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / Num. unique all: 64759 / Rsym value: 0.48 / % possible all: 52.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MIR
Starting model: Original modeling

Resolution: 1.81→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The diffraction images were affected by the severe ice rings whose removal resulted in a loss of ~12% of the measured reflections from the refinement. the perfect merohedral twinning was ...Details: The diffraction images were affected by the severe ice rings whose removal resulted in a loss of ~12% of the measured reflections from the refinement. the perfect merohedral twinning was detected in the crystals with the twinning operator {h,-k,-l}. the refinement statistics presented for this entry corresponds to the refinement carried out using the twinning option of the cns program. for the deposition the diffraction data were detwinned using the cns program. therefore, the refinement statistics calculated based on the detwinned data might be slightly different from those obtained during the "twinned" refinement included in this entry.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3150 -Random
Rwork0.215 ---
all0.218 64759 --
obs0.218 64759 80 %-
Displacement parametersBiso mean: 40.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 4 479 6565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.98
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 1.81→1.87 Å
RfactorNum. reflection% reflection
Rfree0.33 226 -
Rwork0.328 --
obs-4486 52.3 %

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