[English] 日本語
Yorodumi
- PDB-6j6a: Crystal structure of TldE from Thermococcus kodakarensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j6a
TitleCrystal structure of TldE from Thermococcus kodakarensis
ComponentsZinc-dependent protease, TldD/PmbA family
KeywordsMETAL BINDING PROTEIN / metalloprotease
Function / homologyPmbA/TldA metallopeptidase C-terminal domain / Metalloprotease TldD/E, N-terminal domain / Metalloprotease TldD/PmbA, N-terminal / Metalloprotease TldD/PmbA superfamily / PmbA/TldA metallopeptidase domain 1 / PmbA/TldA metallopeptidase central domain / metallopeptidase activity / cytosol / Zinc-dependent protease, TldD/PmbA family
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.353 Å
AuthorsZhang, X. / Liu, J.
CitationJournal: To Be Published
Title: Crystal structure of TldE from Thermococcus kodakarensis
Authors: Zhang, X. / Liu, J.
History
DepositionJan 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Zinc-dependent protease, TldD/PmbA family
B: Zinc-dependent protease, TldD/PmbA family


Theoretical massNumber of molelcules
Total (without water)97,5082
Polymers97,5082
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-6 kcal/mol
Surface area36030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.497, 104.497, 253.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Zinc-dependent protease, TldD/PmbA family


Mass: 48754.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0499 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JD94
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.55 Å3/Da / Density % sol: 65.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.02M Calcium Chloride, 0.1M Sodium Acetate pH 4.6, 30% v/v MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.353→31.931 Å / Num. obs: 59216 / % possible obs: 99.9 % / Redundancy: 11.1 % / CC1/2: 0.996 / Rpim(I) all: 0.052 / Net I/σ(I): 29.67
Reflection shellResolution: 2.353→2.437 Å / Num. unique obs: 2896 / CC1/2: 0.713 / Rpim(I) all: 0.508

-
Processing

Software
NameVersionClassification
PHENIX(1.14rc2_3191: ???)refinement
ADSCdata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VL4

1vl4


Resolution: 2.353→31.931 Å / SU ML: 0.26 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 22.66
RfactorNum. reflection% reflection
Rfree0.2281 2000 3.38 %
Rwork0.1955 --
obs0.1966 59118 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.353→31.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 0 256 7110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086990
X-RAY DIFFRACTIONf_angle_d1.0149456
X-RAY DIFFRACTIONf_dihedral_angle_d4.3364212
X-RAY DIFFRACTIONf_chiral_restr0.0661042
X-RAY DIFFRACTIONf_plane_restr0.0071240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3526-2.41140.28841360.26693884X-RAY DIFFRACTION97
2.4114-2.47660.2971400.28034018X-RAY DIFFRACTION100
2.4766-2.54940.28141420.25464035X-RAY DIFFRACTION100
2.5494-2.63170.27911410.23814020X-RAY DIFFRACTION100
2.6317-2.72570.28441410.22844017X-RAY DIFFRACTION100
2.7257-2.83480.28031410.22964064X-RAY DIFFRACTION100
2.8348-2.96370.26641420.21844021X-RAY DIFFRACTION100
2.9637-3.11980.2621420.21544070X-RAY DIFFRACTION100
3.1198-3.31510.22861430.20314061X-RAY DIFFRACTION100
3.3151-3.57080.22641420.18584092X-RAY DIFFRACTION100
3.5708-3.92950.2171450.17394112X-RAY DIFFRACTION100
3.9295-4.49680.21141440.16874131X-RAY DIFFRACTION100
4.4968-5.66030.1991470.17684195X-RAY DIFFRACTION100
5.6603-31.93420.18111540.1754398X-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://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