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- PDB-1rxd: Crystal structure of human protein tyrosine phosphatase 4A1 -

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Basic information

Entry
Database: PDB / ID: 1rxd
TitleCrystal structure of human protein tyrosine phosphatase 4A1
Componentsprotein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1
Keywordsstructural genomics / unknown function / NYSGXRC / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / spindle / cytoplasmic side of plasma membrane / early endosome / positive regulation of cell migration / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
: / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases domain profile. ...: / Polymorphic toxin system, DSP-PTPase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein tyrosine phosphatase type IVA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSun, J.P. / Fedorov, A.A. / Almo, S.C. / Zhang, Z.Y. / Burley, S.K. / 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
DepositionDec 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 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: protein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1
B: protein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1
C: protein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1


Theoretical massNumber of molelcules
Total (without water)55,2843
Polymers55,2843
Non-polymers00
Water4,792266
1
A: protein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1


Theoretical massNumber of molelcules
Total (without water)18,4281
Polymers18,4281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: protein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1


Theoretical massNumber of molelcules
Total (without water)18,4281
Polymers18,4281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: protein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1


Theoretical massNumber of molelcules
Total (without water)18,4281
Polymers18,4281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.291, 105.568, 179.355
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assemply is a monomer

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Components

#1: Protein protein tyrosine phosphatase type IVA, member 1; Protein tyrosine phosphatase IVA1


Mass: 18427.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q93096
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.216 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911, 0.97934, 0.97166
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.979341
30.971661
ReflectionResolution: 1.9→25 Å / Num. all: 48954 / Num. obs: 48954 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.132 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.2 / % possible all: 72.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→25 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.242 4919 9.2 %
Rwork0.223 --
all0.226 48954 -
obs0.226 48954 91.3 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.8521 Å2 / ksol: 0.358711 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.238 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 0 266 3912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.271.5
X-RAY DIFFRACTIONc_mcangle_it3.572
X-RAY DIFFRACTIONc_scbond_it4.032
X-RAY DIFFRACTIONc_scangle_it6.372.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.364 310 5.9 %
Rwork0.353 2760 -
obs-3070 68.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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