[English] 日本語
Yorodumi
- PDB-5w5g: Structure of Human Sts-1 histidine phosphatase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w5g
TitleStructure of Human Sts-1 histidine phosphatase domain
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


regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / 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 ...regulation of osteoclast differentiation / collagen-activated tyrosine kinase receptor signaling pathway / 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 / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Ubiquitin associated domain / Histidine phosphatase superfamily / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...UBASH3B, SH3 domain / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / UBA/TS-N domain / Variant SH3 domain / Ubiquitin associated 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 B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.48 Å
AuthorsZhou, W. / Yin, Y. / Weinheimer, A.W. / Kaur, N. / Carpino, N. / French, J.B.
Funding support United States, 5items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH17-1-0147 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)U01HL127522 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10 RR029205 United States
National Institutes of Health/Office of the DirectorS10OD021527 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
DepositionJun 15, 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 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,5783
Polymers88,5783
Non-polymers00
Water1,71195
1
A: Ubiquitin-associated and SH3 domain-containing protein B
B: Ubiquitin-associated and SH3 domain-containing protein B


Theoretical massNumber of molelcules
Total (without water)59,0522
Polymers59,0522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-22 kcal/mol
Surface area22200 Å2
MethodPISA
2
C: Ubiquitin-associated and SH3 domain-containing protein B

C: Ubiquitin-associated and SH3 domain-containing protein B


Theoretical massNumber of molelcules
Total (without water)59,0522
Polymers59,0522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2700 Å2
ΔGint-20 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.602, 74.498, 101.720
Angle α, β, γ (deg.)90.000, 100.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-752-

HOH

-
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: 29525.904 Da / Num. of mol.: 3 / Fragment: UNP Residues 383-644
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Hepes, pH 7 5% ethylene glycol 0.3 M magnesium chloride 13% PEG 8000

-
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: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 28546 / % possible obs: 93.8 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.089 / Rrim(I) all: 0.146 / Χ2: 2.076 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.49-2.532.10.490.5870.3880.6291.09593.9
2.53-2.5820.40.6970.3220.5161.03892.7
2.58-2.632.20.3830.7550.2960.4861.13495.5
2.63-2.682.30.3520.7640.2740.4481.27295.7
2.68-2.742.30.3290.7690.2520.4161.55894.4
2.74-2.82.30.3110.7940.2380.3941.75695.8
2.8-2.872.30.2730.8320.2140.3491.96995.2
2.87-2.952.30.2460.8560.190.3122.31794.2
2.95-3.042.20.2260.8730.1750.2882.42293.3
3.04-3.142.10.2080.8470.1670.2682.47392
3.14-3.252.20.2040.8740.1590.262.53493.9
3.25-3.382.40.1880.9180.1440.2392.40695.4
3.38-3.532.40.1770.9090.1340.2232.57894.1
3.53-3.722.30.1660.8990.1290.2112.53393.6
3.72-3.952.30.1490.9210.1170.1912.46393.4
3.95-4.262.10.130.9170.1050.1682.37391.6
4.26-4.692.30.1160.9460.090.1482.5393.6
4.69-5.362.30.1120.9480.0870.1432.5193.6
5.36-6.762.30.0830.9770.0640.1052.18491.7
6.76-752.40.0740.9850.0560.0932.0591.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

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

3d4i


Resolution: 2.48→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.614 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.656 / ESU R Free: 0.3
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1441 5 %RANDOM
Rwork0.1943 ---
obs0.1971 27105 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.83 Å2 / Biso mean: 66.519 Å2 / Biso min: 35.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0 Å2-0.65 Å2
2--1.53 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 2.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5816 0 0 98 5914
Biso mean---62.6 -
Num. residues----771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195965
X-RAY DIFFRACTIONr_bond_other_d0.0010.025454
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.9528151
X-RAY DIFFRACTIONr_angle_other_deg0.734312502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1275768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.32923.473239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68415883
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3621534
X-RAY DIFFRACTIONr_chiral_restr0.0550.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021382
LS refinement shellResolution: 2.479→2.543 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 83 -
Rwork0.242 1889 -
all-1972 -
obs--89.07 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more