[English] 日本語
Yorodumi
- PDB-4urj: Crystal structure of human BJ-TSA-9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4urj
TitleCrystal structure of human BJ-TSA-9
ComponentsPROTEIN FAM83A
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


phosphatidylinositol 3-kinase regulatory subunit binding / epidermal growth factor receptor signaling pathway / cell population proliferation / protein kinase binding / signal transduction / identical protein binding / cytoplasm
Similarity search - Function
FAM83, N-terminal / FAM83 A-H / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsPinkas, D.M. / Sanvitale, C. / Wang, D. / Krojer, T. / Kopec, J. / Chaikuad, A. / Dixon Clarke, S. / Berridge, G. / Burgess-Brown, N. / von Delft, F. ...Pinkas, D.M. / Sanvitale, C. / Wang, D. / Krojer, T. / Kopec, J. / Chaikuad, A. / Dixon Clarke, S. / Berridge, G. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Bullock, A.
CitationJournal: To be Published
Title: Crystal Structure of Human Bj-Tsa-9
Authors: Pinkas, D.M. / Sanvitale, C. / Wang, D. / Krojer, T. / Kopec, J. / Chaikuad, A. / Dixon Clarke, S. / Berridge, G. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Bullock, A.
History
DepositionJun 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN FAM83A
B: PROTEIN FAM83A
C: PROTEIN FAM83A
D: PROTEIN FAM83A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,10911
Polymers84,6744
Non-polymers4347
Water1,856103
1
A: PROTEIN FAM83A
hetero molecules

B: PROTEIN FAM83A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4614
Polymers42,3372
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3050 Å2
ΔGint-10 kcal/mol
Surface area15620 Å2
MethodPISA
2
C: PROTEIN FAM83A
D: PROTEIN FAM83A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6477
Polymers42,3372
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-7 kcal/mol
Surface area16300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.120, 50.730, 120.290
Angle α, β, γ (deg.)90.00, 105.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
PROTEIN FAM83A / BJ-TSA-9 / TUMOR ANTIGEN BJ-TSA-9 / TUMOR-SPECIFIC GENE EXPRESSED IN PROSTATE PROTEIN


Mass: 21168.578 Da / Num. of mol.: 4 / Fragment: DUF1669, UNP RESIDUES 122-304
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q86UY5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growDetails: 0.8M SODIUM PHOSPHATE MONOBASIC, 0.8M SODIUM PHOSPHATE DIBASIC, 0.1M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.68→42.08 Å / Num. obs: 25987 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 31.31 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 3.4
Reflection shellResolution: 2.68→2.81 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
RosettaMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→42.084 Å / SU ML: 0.39 / σ(F): 1.97 / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 1992 7.7 %
Rwork0.2323 --
obs0.2349 25835 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.44 Å2
Refinement stepCycle: LAST / Resolution: 2.68→42.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5421 0 28 103 5552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055543
X-RAY DIFFRACTIONf_angle_d0.7447457
X-RAY DIFFRACTIONf_dihedral_angle_d10.721994
X-RAY DIFFRACTIONf_chiral_restr0.028849
X-RAY DIFFRACTIONf_plane_restr0.003937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6801-2.74710.38031380.33111649X-RAY DIFFRACTION99
2.7471-2.82130.38861430.31511723X-RAY DIFFRACTION99
2.8213-2.90430.34241420.29361675X-RAY DIFFRACTION99
2.9043-2.99810.33021420.27981708X-RAY DIFFRACTION99
2.9981-3.10520.31331400.2691683X-RAY DIFFRACTION100
3.1052-3.22950.31291410.26141685X-RAY DIFFRACTION99
3.2295-3.37640.29161410.25781684X-RAY DIFFRACTION100
3.3764-3.55430.2871430.22691704X-RAY DIFFRACTION100
3.5543-3.77690.21571410.21831686X-RAY DIFFRACTION100
3.7769-4.06830.23191420.21061704X-RAY DIFFRACTION100
4.0683-4.47720.21851440.19081720X-RAY DIFFRACTION100
4.4772-5.12410.19461430.17081717X-RAY DIFFRACTION99
5.1241-6.45210.24321450.20911734X-RAY DIFFRACTION100
6.4521-42.08870.25161470.22321771X-RAY DIFFRACTION98

+
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://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