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- PDB-5vr6: Structure of Human Sts-1 histidine phosphatase domain with sulfat... -

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Basic information

Entry
Database: PDB / ID: 5vr6
TitleStructure of Human Sts-1 histidine phosphatase domain with sulfate bound
ComponentsUbiquitin-associated and SH3 domain-containing protein B
KeywordsHYDROLASE / T-Cell Receptor / histidine phosphatase / protein tyrosine phosphatase / Zap-70
Function / homology
Function and homology information


collagen-activated tyrosine kinase receptor signaling pathway / regulation of osteoclast differentiation / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding ...collagen-activated tyrosine kinase receptor signaling pathway / regulation of osteoclast differentiation / negative regulation of platelet aggregation / regulation of release of sequestered calcium ion into cytosol / negative regulation of bone resorption / negative regulation of osteoclast differentiation / negative regulation of signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / phosphoprotein binding / platelet aggregation / ubiquitin protein ligase binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
UBASH3B, SH3 domain / : / UBA-like 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 ...UBASH3B, SH3 domain / : / UBA-like 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 / 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 B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsZhou, W. / Yin, Y. / Weinheimer, A.W. / Kaur, N. / Carpino, N. / French, J.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)U01HL127522 United States
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
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Refinement description / Category: citation / software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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


Theoretical massNumber of molelcules
Total (without water)61,50018
Polymers59,9632
Non-polymers1,53716
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-305 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.640, 79.160, 105.102
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin-associated and SH3 domain-containing protein B / Cbl-interacting protein p70 / Suppressor of T-cell receptor signaling 1 / STS-1 / T-cell ubiquitin ...Cbl-interacting protein p70 / Suppressor of T-cell receptor signaling 1 / STS-1 / T-cell ubiquitin ligand 2 / TULA-2 / Tyrosine-protein phosphatase STS1/TULA2


Mass: 29981.387 Da / Num. of mol.: 2 / Fragment: UNP Residues 384-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBASH3B, KIAA1959, STS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TF42, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 22 - 25% PEG 2000 MME 200 mM Ammonium Sulfate 0.1 M Sodium Acetate
PH range: 5 - 5.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 41518 / % possible obs: 94.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.037 / Rrim(I) all: 0.086 / Χ2: 0.601 / Net I/σ(I): 4.9 / Num. measured all: 211226
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.87-1.94.10.2030.9730.1090.2320.47877.7
1.9-1.944.70.1850.9870.0920.2080.47581.3
1.94-1.974.90.1730.9850.0820.1920.47785.4
1.97-2.0150.1750.9870.0830.1950.48887.4
2.01-2.065.10.1620.9870.0770.180.49388.6
2.06-2.1150.1460.9920.0690.1620.51591.4
2.11-2.1650.1430.9890.070.160.52291.9
2.16-2.224.80.1370.9870.0680.1540.53691.9
2.22-2.285.10.130.9910.0630.1450.54996.9
2.28-2.365.30.1240.9930.0590.1380.54998.1
2.36-2.445.30.1180.9920.0560.1310.58499.5
2.44-2.545.30.1140.9930.0540.1270.57699.8
2.54-2.655.10.1040.9940.0510.1160.60199.5
2.65-2.795.10.0950.9940.0460.1050.59399.8
2.79-2.975.50.0810.9960.0380.090.639100
2.97-3.25.40.0730.9960.0350.0810.66899.8
3.2-3.5250.0610.9970.030.0680.73399.3
3.52-4.035.50.0520.9980.0240.0570.851100
4.03-5.075.20.0490.9970.0240.0550.87599.8
5.07-5050.0410.9980.020.0460.59699.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
d*TREKdata scaling
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
d*TREKdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H0Q

2h0q


Resolution: 1.87→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.354 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24101 2033 4.9 %RANDOM
Rwork0.19424 ---
obs0.19655 39429 94.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.628 Å2
Baniso -1Baniso -2Baniso -3
1--2.69 Å2-0 Å20 Å2
2--4.72 Å20 Å2
3----2.03 Å2
Refinement stepCycle: 1 / Resolution: 1.87→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 80 336 4556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194339
X-RAY DIFFRACTIONr_bond_other_d0.0010.023983
X-RAY DIFFRACTIONr_angle_refined_deg1.1151.975924
X-RAY DIFFRACTIONr_angle_other_deg0.76139178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30423.71186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39815696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8811526
X-RAY DIFFRACTIONr_chiral_restr0.0650.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02997
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_it0.8791.9842128
X-RAY DIFFRACTIONr_mcbond_other0.8771.9832127
X-RAY DIFFRACTIONr_mcangle_it1.5122.9682659
X-RAY DIFFRACTIONr_mcangle_other1.5122.9692660
X-RAY DIFFRACTIONr_scbond_it1.032.1712211
X-RAY DIFFRACTIONr_scbond_other0.9552.1092144
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5933.1223163
X-RAY DIFFRACTIONr_long_range_B_refined4.29416.5065189
X-RAY DIFFRACTIONr_long_range_B_other4.12516.3465090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.869→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 120 -
Rwork0.219 2317 -
obs--76.25 %

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