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- PDB-3d8k: Crystal structure of a phosphatase from a toxoplasma gondii -

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Basic information

Entry
Database: PDB / ID: 3d8k
TitleCrystal structure of a phosphatase from a toxoplasma gondii
ComponentsProtein phosphatase 2C
KeywordsHYDROLASE / 9110a1 / NYSGRC / PSI-II / Phosphatase / Toxoplasma gondii. / Structural Genomics / Protein Structure Initiative / New York Structural GenomiX Research Consortium / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


protein serine/threonine phosphatase activity
Similarity search - Function
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
Protein phosphatase 2C
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.71 Å
AuthorsDamodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crsytal structure of a phosphatase from a toxoplasma gondii
Authors: Damodharan, L. / Sauder, J.M. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Structure summary
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Nov 14, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Jan 16, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.6Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein phosphatase 2C
B: Protein phosphatase 2C
C: Protein phosphatase 2C
D: Protein phosphatase 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,4358
Polymers168,0514
Non-polymers3844
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-23 kcal/mol
Surface area59060 Å2
Unit cell
Length a, b, c (Å)57.882, 169.052, 87.012
Angle α, β, γ (deg.)90.00, 104.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein phosphatase 2C / PP2C


Mass: 42012.773 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: pp2c / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3(RIPL) / References: UniProt: A4GX63
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M Ammonium sulphate, 0.1 Sodium acetate pH 4.6, 30% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 14, 2007 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 48537 / Num. obs: 48537 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2 / Num. unique all: 4348 / % possible all: 87.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.71→46.71 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 95601.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1052 2.5 %RANDOM
Rwork0.251 ---
all0.278 48537 --
obs0.251 41520 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.872 Å2 / ksol: 0.32378 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-11.9 Å20 Å23.75 Å2
2---2.19 Å20 Å2
3----9.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.71→46.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10691 0 20 181 10892
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 2.71→2.88 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.437 159 2.6 %
Rwork0.358 5935 -
obs--83.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4_xplor.parso4_xplor.top
X-RAY DIFFRACTION4ion.paramion.top

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