[English] 日本語
Yorodumi
- PDB-6izb: Flexible loop truncated human TCTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6izb
TitleFlexible loop truncated human TCTP
ComponentsTranslationally-controlled tumor protein
KeywordsIMMUNE SYSTEM / alpha/beta fold / flexible loop truncated / dimer / disulfide bond
Function / homology
Function and homology information


negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cytoplasmic microtubule / multivesicular body / response to virus / intracellular calcium ion homeostasis / spindle pole / calcium ion transport / regulation of apoptotic process / calcium ion binding / negative regulation of apoptotic process ...negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / cytoplasmic microtubule / multivesicular body / response to virus / intracellular calcium ion homeostasis / spindle pole / calcium ion transport / regulation of apoptotic process / calcium ion binding / negative regulation of apoptotic process / extracellular space / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
Translationally controlled tumor protein (TCTP) domain signature 1. / Translationally controlled tumour protein, conserved site / Translationally controlled tumor protein (TCTP) domain signature 2. / Translationally controlled tumour protein / Translationally controlled tumour protein (TCTP) domain / Translationally controlled tumour protein / Translationally controlled tumor protein (TCTP) domain profile. / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily
Similarity search - Domain/homology
Translationally-controlled tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 1.899 Å
AuthorsShin, D.H. / Kim, M.S.
CitationJournal: To Be Published
Title: Flexible loop truncated human TCTP
Authors: Shin, D.H. / Kim, M.S.
History
DepositionDec 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Translationally-controlled tumor protein


Theoretical massNumber of molelcules
Total (without water)17,9591
Polymers17,9591
Non-polymers00
Water1,63991
1
A: Translationally-controlled tumor protein

A: Translationally-controlled tumor protein


Theoretical massNumber of molelcules
Total (without water)35,9172
Polymers35,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area2190 Å2
ΔGint-10 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.295, 69.295, 146.062
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-235-

HOH

21A-268-

HOH

31A-290-

HOH

-
Components

#1: Protein Translationally-controlled tumor protein / TCTP / Fortilin / Histamine-releasing factor / HRF / p23


Mass: 17958.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TPT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13693
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 25 % (w/v) PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: May 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→46.37 Å / Num. obs: 17029 / % possible obs: 99.5 % / Redundancy: 36.1 % / Net I/σ(I): 45.7
Reflection shellResolution: 1.9→1.97 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
pointlessdata scaling
PHENIXphasing
RefinementResolution: 1.899→46.366 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 852 5 %
Rwork0.2196 --
obs0.2209 17028 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→46.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 0 91 1308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191242
X-RAY DIFFRACTIONf_angle_d1.1871663
X-RAY DIFFRACTIONf_dihedral_angle_d18.322478
X-RAY DIFFRACTIONf_chiral_restr0.069174
X-RAY DIFFRACTIONf_plane_restr0.009214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8991-2.01810.29281340.25312543X-RAY DIFFRACTION97
2.0181-2.17390.27661390.23722655X-RAY DIFFRACTION100
2.1739-2.39270.2691400.2212662X-RAY DIFFRACTION100
2.3927-2.73890.23241400.21942676X-RAY DIFFRACTION100
2.7389-3.45050.25531450.22212728X-RAY DIFFRACTION100
3.4505-46.37940.2311540.21152912X-RAY DIFFRACTION100

+
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