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- PDB-2y96: Structure of human dual-specificity phosphatase 27 -

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Basic information

Entry
Database: PDB / ID: 2y96
TitleStructure of human dual-specificity phosphatase 27
ComponentsDUAL SPECIFICITY PHOSPHATASE DUPD1
KeywordsHYDROLASE
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / protein-serine/threonine phosphatase / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein homodimerization activity / protein-containing complex / cytoplasm
Similarity search - Function
: / Atypical dual specificity phosphatase, subfamily A / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. ...: / Atypical dual specificity phosphatase, subfamily A / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / 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 phosphatase DUPD1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsLountos, G.T. / Tropea, J.E. / Waugh, D.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of Human Dual-Specificity Phosphatase at 2.38A Resolution
Authors: Lountos, G.T. / Tropea, J.E. / Waugh, D.S.
History
DepositionFeb 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1May 26, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: DUAL SPECIFICITY PHOSPHATASE DUPD1
B: DUAL SPECIFICITY PHOSPHATASE DUPD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1539
Polymers50,4812
Non-polymers6727
Water2,468137
1
A: DUAL SPECIFICITY PHOSPHATASE DUPD1
B: DUAL SPECIFICITY PHOSPHATASE DUPD1
hetero molecules

A: DUAL SPECIFICITY PHOSPHATASE DUPD1
B: DUAL SPECIFICITY PHOSPHATASE DUPD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,30618
Polymers100,9624
Non-polymers1,34514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area12720 Å2
ΔGint-281.5 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.012, 126.012, 125.758
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein DUAL SPECIFICITY PHOSPHATASE DUPD1 / HUMAN DUAL-SPECIFICITY PHOSPHATASE 27


Mass: 25240.379 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PJT154 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q68J44, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.86 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 6
Details: 10 MG/ML PROTEIN, 0.2M AMMONIUM SULFATE, 25% W/V PEG3350, ROOM TEMPERATURE, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 24047 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 16.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 48.2
Reflection shellResolution: 2.38→2.43 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PQ5

2pq5


Resolution: 2.38→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.924 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22482 1220 5.1 %RANDOM
Rwork0.20139 ---
obs0.20257 22618 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 35 137 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222872
X-RAY DIFFRACTIONr_bond_other_d0.0010.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9573899
X-RAY DIFFRACTIONr_angle_other_deg0.91234676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1075341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4123.014146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67315474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2641525
X-RAY DIFFRACTIONr_chiral_restr0.0920.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7521.51703
X-RAY DIFFRACTIONr_mcbond_other0.1531.5684
X-RAY DIFFRACTIONr_mcangle_it1.44822741
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.20631169
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4824.51157
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.384→2.446 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 86 -
Rwork0.252 1596 -
obs--97.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.22020.3571-0.7883-0.01120.37080.26150.10730.12370.634-0.22250.0037-0.0039-0.4656-0.0608-0.11110.44340.09820.11770.41940.08090.1948-15.295-32.826-7.507
22.50830.4672-0.14972.41410.48451.67610.08870.1415-0.0455-0.2752-0.1199-0.0744-0.0674-0.02570.03120.21660.10210.05940.44350.01460.1093-22.551-48.169-6.85
33.2269-0.6565-1.85670.3772-0.75212.8827-0.16640.0934-0.3316-0.07690.17680.22240.2195-0.0868-0.01040.2273-0.09010.08090.4216-0.04410.2180.897-57.384-15.987
42.96940.8254-0.05483.02920.22845.1858-0.04490.18840.1026-0.10190.02570.0916-0.61920.0150.01920.2229-0.09140.10630.37380.01340.11578.081-43.245-21.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 103
2X-RAY DIFFRACTION2A104 - 205
3X-RAY DIFFRACTION3B32 - 103
4X-RAY DIFFRACTION4B104 - 201

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