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- PDB-2nt2: Crystal Structure of Slingshot phosphatase 2 -

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Basic information

Entry
Database: PDB / ID: 2nt2
TitleCrystal Structure of Slingshot phosphatase 2
ComponentsProtein phosphatase Slingshot homolog 2
KeywordsHYDROLASE / alpha/beta hydrolase
Function / homology
Function and homology information


negative regulation of actin filament polymerization / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / acrosomal vesicle / protein tyrosine phosphatase activity / actin binding / actin cytoskeleton organization ...negative regulation of actin filament polymerization / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / acrosomal vesicle / protein tyrosine phosphatase activity / actin binding / actin cytoskeleton organization / spermatogenesis / cell differentiation / cytoskeleton / focal adhesion / extracellular space / cytoplasm
Similarity search - Function
Protein phosphatase Slingshot-like / Slingshot, N-terminal / DEK C terminal domain / DEK, C-terminal / DEK C-terminal (DEK-C) domain profile. / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain ...Protein phosphatase Slingshot-like / Slingshot, N-terminal / DEK C terminal domain / DEK, C-terminal / DEK C-terminal (DEK-C) domain profile. / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / 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 / 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
Protein phosphatase Slingshot homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJung, S.K. / Jeong, D.G. / Yoon, T.S. / Kim, J.H. / Ryu, S.E. / Kim, S.J.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of human slingshot phosphatase 2.
Authors: Jung, S.K. / Jeong, D.G. / Yoon, T.S. / Kim, J.H. / Ryu, S.E. / Kim, S.J.
History
DepositionNov 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein phosphatase Slingshot homolog 2
B: Protein phosphatase Slingshot homolog 2
C: Protein phosphatase Slingshot homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4936
Polymers51,2053
Non-polymers2883
Water1,63991
1
A: Protein phosphatase Slingshot homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1642
Polymers17,0681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein phosphatase Slingshot homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1642
Polymers17,0681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein phosphatase Slingshot homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1642
Polymers17,0681
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.58, 94.58, 38.77
Angle α, β, γ (deg.)90, 90, 120
Int Tables number145
Space group name H-MP32
DetailsThe biological assembly is monomer

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Components

#1: Protein Protein phosphatase Slingshot homolog 2 / Slingshot phosphatase 2 / SSH-2L / hSSH-2L


Mass: 17068.248 Da / Num. of mol.: 3 / Fragment: Catalytic domain, residues 305-449 / Mutation: C392S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSH2, KIAA1725, SSH2L / Plasmid: pET28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q76I76, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.95 Å3/Da / Density % sol: 37.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, pH 8.5, 25% PEG3350, 8% Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2005 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 22566 / Num. obs: 22566 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3301 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VHR

1vhr


Resolution: 2.1→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1128 -RANDOM
Rwork0.142 ---
all0.144 22563 --
obs0.144 22563 99.1 %-
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3528 0 15 91 3634
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d1.37
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_from_restr_planes0.348
X-RAY DIFFRACTIONs_zero_chiral_vol0.048

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