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- PDB-5wdi: Structure of Human Sts-2 histidine phosphatase domain -

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Basic information

Entry
Database: PDB / ID: 5wdi
TitleStructure of Human Sts-2 histidine phosphatase domain
ComponentsUbiquitin-associated and SH3 domain-containing protein A
KeywordsHYDROLASE / T-Cell Receptor / histidine phosphatase / protein tyrosine phosphatase / Zap-70
Function / homology
Function and homology information


negative regulation of T cell receptor signaling pathway / regulation of cytokine production / nuclear speck / extracellular exosome / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
UBASH3A, SH3 domain / : / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Variant SH3 domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily ...UBASH3A, SH3 domain / : / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Variant SH3 domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-associated and SH3 domain-containing protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsZhou, W. / Yin, Y. / Weinheimer, A.W. / Kaur, N. / Carpino, N. / French, J.B.
CitationJournal: Biochemistry / Year: 2017
Title: Structural and Functional Characterization of the Histidine Phosphatase Domains of Human Sts-1 and Sts-2.
Authors: Zhou, W. / Yin, Y. / Weinheimer, A.S. / Kaur, N. / Carpino, N. / French, J.B.
History
DepositionJul 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-associated and SH3 domain-containing protein A
B: Ubiquitin-associated and SH3 domain-containing protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1437
Polymers59,6632
Non-polymers4805
Water2,144119
1
A: Ubiquitin-associated and SH3 domain-containing protein A
hetero molecules

B: Ubiquitin-associated and SH3 domain-containing protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1437
Polymers59,6632
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4500 Å2
ΔGint-32 kcal/mol
Surface area21860 Å2
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-8 kcal/mol
Surface area24910 Å2
Unit cell
Length a, b, c (Å)77.507, 113.115, 60.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-702-

SO4

21A-876-

HOH

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Components

#1: Protein Ubiquitin-associated and SH3 domain-containing protein A / Cbl-interacting protein 4 / CLIP4 / Suppressor of T-cell receptor signaling 2 / STS-2 / T-cell ...Cbl-interacting protein 4 / CLIP4 / Suppressor of T-cell receptor signaling 2 / STS-2 / T-cell ubiquitin ligand 1 / TULA-1


Mass: 29831.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBASH3A, STS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P57075
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, pH 7.0 22% PEG 4000 0.2 M potassium acetate 0.2 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 20513 / % possible obs: 98.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.055 / Rrim(I) all: 0.107 / Χ2: 1.028 / Net I/σ(I): 7.7 / Num. measured all: 74181
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.43-2.473.40.5689580.7450.3530.6710.74194.2
2.47-2.523.50.6020.7890.3660.7070.79795.4
2.52-2.573.60.4630.8520.2750.5410.74294.3
2.57-2.623.60.4510.8530.2670.5260.79697.4
2.62-2.673.70.4060.8760.2390.4730.82995.6
2.67-2.743.60.3390.9130.20.3950.83899.2
2.74-2.813.70.2870.9270.1690.3340.85197.6
2.81-2.883.60.2270.9540.1350.2650.85799.6
2.88-2.973.70.2090.9630.1230.2430.89698.6
2.97-3.063.70.1780.9720.1060.2071.05498.4
3.06-3.173.70.1450.9810.0850.1681.04100
3.17-3.33.70.1210.9850.0720.1411.13199.1
3.3-3.453.70.10.9870.0590.1171.23499.2
3.45-3.633.70.0760.9930.0450.0891.35999.4
3.63-3.863.70.0690.9920.0420.0811.37699.5
3.86-4.153.60.0590.9930.0360.071.48299.6
4.15-4.573.60.0540.9940.0340.0641.56699.5
4.57-5.233.50.0460.9960.0280.0541.25699.5
5.23-6.593.60.0440.9970.0270.0510.9999.8
6.59-503.40.0240.9990.0150.0290.59398.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D4I

3d4i


Resolution: 2.43→63.94 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / SU B: 10.05 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.626 / ESU R Free: 0.288
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 996 4.9 %RANDOM
Rwork0.2035 ---
obs0.2058 19484 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98 Å2 / Biso mean: 38.305 Å2 / Biso min: 16.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20 Å2
2--3.06 Å2-0 Å2
3----2.87 Å2
Refinement stepCycle: final / Resolution: 2.43→63.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 25 119 4187
Biso mean--71.97 32.67 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194158
X-RAY DIFFRACTIONr_bond_other_d0.0010.023909
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.9755653
X-RAY DIFFRACTIONr_angle_other_deg0.72439006
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4565520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48623.45171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28715682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2261531
X-RAY DIFFRACTIONr_chiral_restr0.0590.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02921
LS refinement shellResolution: 2.43→2.493 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 76 -
Rwork0.283 1334 -
all-1410 -
obs--93.25 %

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