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- PDB-2isn: Crystal structure of a phosphatase from a pathogenic strain Toxop... -

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Basic information

Entry
Database: PDB / ID: 2isn
TitleCrystal structure of a phosphatase from a pathogenic strain Toxoplasma gondii
ComponentsNYSGXRC-8828z, phosphatase
KeywordsHYDROLASE / 8828z / phosphatase / pathogenic strain / praseodymium / sulfate / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyPPM-type phosphatase domain / Phosphatase 2c; domain 1 / 4-Layer Sandwich / Alpha Beta / PRASEODYMIUM ION
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2007
Title: Structural genomics of protein phosphatases.
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionOct 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NYSGXRC-8828z, phosphatase
B: NYSGXRC-8828z, phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0317
Polymers80,4612
Non-polymers5705
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-83 kcal/mol
Surface area27550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.986, 62.447, 63.738
Angle α, β, γ (deg.)65.53, 70.21, 77.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NYSGXRC-8828z, phosphatase


Mass: 40230.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Plasmid: pSGX4(BS) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 2M Li2So4, 0.5M Ammonium sulfate, 0.1M Na-citrate, ph 5.6, praseodymium acetate, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C10.9792, 0.9788,0.9500
SYNCHROTRONNSLS X2520.9801
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDSep 22, 2006mirrors
ADSC QUANTUM 3152CCDOct 1, 2006mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1si(111)MADMx-ray1
2si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97881
30.951
40.98011
ReflectionResolution: 1.9→50 Å / Num. all: 54775 / Num. obs: 54775 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1 / Num. unique all: 5424 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 1.9→43.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 68658.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: the missing residues listed in Remark 465 are due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1604 3 %RANDOM
Rwork0.241 ---
obs0.241 53112 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.6401 Å2 / ksol: 0.35205 e/Å3
Displacement parametersBiso mean: 13.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å2-2.22 Å22.84 Å2
2---1.57 Å2-0.17 Å2
3---0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.9→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 17 252 5353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 262 3.1 %
Rwork0.244 8089 -
obs-54775 91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramprese-new.top
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4prese-new.param

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