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- PDB-1mkp: CRYSTAL STRUCTURE OF PYST1 (MKP3) -

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Basic information

Entry
Database: PDB / ID: 1mkp
TitleCRYSTAL STRUCTURE OF PYST1 (MKP3)
ComponentsPYST1
KeywordsHYDROLASE
Function / homology
Function and homology information


regulation of heart growth / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / response to nitrosative stress / protein tyrosine/serine/threonine phosphatase activity / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / ERKs are inactivated / response to growth factor ...regulation of heart growth / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / response to nitrosative stress / protein tyrosine/serine/threonine phosphatase activity / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / ERKs are inactivated / response to growth factor / negative regulation of MAPK cascade / myosin phosphatase activity / protein-serine/threonine phosphatase / peptidyl-tyrosine dephosphorylation / ERK1 and ERK2 cascade / protein-tyrosine-phosphatase / negative regulation of protein phosphorylation / protein tyrosine phosphatase activity / response to organic cyclic compound / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / MAPK cascade / cell differentiation / response to xenobiotic stimulus / positive regulation of apoptotic process / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Dual specificity protein phosphatase 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.35 Å
AuthorsStewart, A.E. / Dowd, S. / Keyse, S. / Mcdonald, N.Q.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of the MAPK phosphatase Pyst1 catalytic domain and implications for regulated activation.
Authors: Stewart, A.E. / Dowd, S. / Keyse, S.M. / McDonald, N.Q.
History
DepositionJul 11, 1998Processing site: BNL
Revision 1.0Jul 22, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYST1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4283
Polymers16,2751
Non-polymers1542
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.000, 90.000, 68.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PYST1 / DUAL SPECIFICITY PHOSPHATASE / MAP KINASE PHOSPHATASE 3 / MKP-3


Mass: 16274.654 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: C293S
Source method: isolated from a genetically manipulated source
Details: MPD AND CHLORIDE ION / Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET14B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q16828, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 4.25 Å3/Da / Density % sol: 71 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 M1reservoirNaCl
2100 mMTris-HCl1reservoir
31 %MPD1reservoir
45 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.35→20 Å / Num. obs: 12163 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 47 Å2 / Rsym value: 0.039 / Net I/σ(I): 11.8
Reflection shellResolution: 2.35→2.45 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.178 / % possible all: 99
Reflection
*PLUS
Num. measured all: 95185 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.178

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
HKLdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.35→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 -5 %RANDOM
Rwork0.201 ---
obs0.201 12163 99.8 %-
Displacement parametersBiso mean: 44 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å2--
2--2.26 Å2-
3---2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 9 39 1234
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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