[English] 日本語
Yorodumi
- PDB-3eop: Crystal Structure of the DUF55 domain of human thymocyte nuclear ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3eop
TitleCrystal Structure of the DUF55 domain of human thymocyte nuclear protein 1
ComponentsThymocyte nuclear protein 1
KeywordsUNKNOWN FUNCTION / Nucleus / Phosphoprotein
Function / homology
Function and homology information


: / EVE domain / EVE domain / ph1033 like fold / ph1033 like domains / PUA-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Thymocyte nuclear protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsYu, F. / Song, A. / Xu, C. / Sun, L. / Li, L. / Tang, L. / Hu, H. / He, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry
Authors: Yu, F. / Song, A. / Xu, C. / Sun, L. / Li, J. / Tang, L. / Yu, M. / Yeates, T.O. / Hu, H. / He, J.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thymocyte nuclear protein 1
B: Thymocyte nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9266
Polymers41,5412
Non-polymers3844
Water66737
1
A: Thymocyte nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9633
Polymers20,7711
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thymocyte nuclear protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9633
Polymers20,7711
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.258, 51.258, 122.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein Thymocyte nuclear protein 1 / Thymocyte protein Thy28


Mass: 20770.738 Da / Num. of mol.: 2 / Fragment: DUF55 domain, UNP residues 55-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) pLysS / References: UniProt: Q9P016
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 10.9
Details: 0.1M NaAc (pH 4.0-4.8), 28% PEG 2000 MME, 200mM (NH4)2SO4, 3% 1,6-diaminohexane as additive, pH 10.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.41 Å / Num. all: 15997 / Num. obs: 15931 / % possible obs: 99.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 40.06 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.291 / Num. unique all: 2326 / % possible all: 98.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ar1

2ar1


Resolution: 2.3→44.39 Å / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 0 / σ(F): 0
Details: Thin resolution shells. Quadruplets of twin related reflections were kept together in either the test set or the refinement set throughout refinement.
RfactorNum. reflection% reflection
Rfree0.2378 1422 8.2 %
Rwork0.1823 --
obs-15463 96.7 %
Solvent computationBsol: 59.208 Å2
Displacement parametersBiso max: 68.11 Å2 / Biso mean: 36.2394 Å2 / Biso min: 5.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.031 Å2-0.085 Å2-0 Å2
2--0.031 Å2-0 Å2
3----0.062 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 20 37 2776
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4071.5
X-RAY DIFFRACTIONc_scbond_it1.7562
X-RAY DIFFRACTIONc_mcangle_it2.2962
X-RAY DIFFRACTIONc_scangle_it2.4452.5
X-RAY DIFFRACTIONc_bond_d0.00602
X-RAY DIFFRACTIONc_angle_d1.17062
X-RAY DIFFRACTIONc_dihedral_angle_d22.63209
X-RAY DIFFRACTIONo_improper_angle_d0.79878
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.3186 119 -
Rwork0.2513 --
obs-1255 91.36 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

+
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