[English] 日本語
Yorodumi
- PDB-3zid: CetZ from Methanosaeta thermophila strain DSM 6194 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zid
TitleCetZ from Methanosaeta thermophila strain DSM 6194
ComponentsTUBULIN/FTSZ, GTPASE
KeywordsGTP-BINDING PROTEIN / TUBZ / PHUZ / CYTOSKELETON
Function / homology
Function and homology information


regulation of cell shape / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Tubulin-like protein CetZ / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Tubulin-like protein CetZ
Similarity search - Component
Biological speciesMETHANOSAETA THERMOPHILA (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAylett, C.H.S. / Amos, L.A. / Lowe, J.
CitationJournal: Nature / Year: 2015
Title: Cetz Tubulin-Like Proteins Control Archaeal Cell Shape
Authors: Duggin, I.G. / Aylett, C.H.S. / Walsh, J.C. / Michie, K.A. / Wang, Q. / Turnbull, L. / Dawson, E.M. / Harry, E.J. / Whitchurch, C.B. / Amos, A. / Lowe, J.
History
DepositionJan 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Mar 25, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TUBULIN/FTSZ, GTPASE
B: TUBULIN/FTSZ, GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1674
Polymers84,2812
Non-polymers8862
Water3,333185
1
A: TUBULIN/FTSZ, GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5832
Polymers42,1401
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TUBULIN/FTSZ, GTPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5832
Polymers42,1401
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.547, 107.011, 76.966
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

-
Components

#1: Protein TUBULIN/FTSZ, GTPASE / CETZ


Mass: 42140.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXA-HISTIDINE TAG / Source: (gene. exp.) METHANOSAETA THERMOPHILA (archaea) / Strain: DSM 6194 / PT / Description: DSM / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0B5R2
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.22 Å3/Da / Density % sol: 44.64 % / Description: NONE
Crystal growpH: 7.5
Details: 30% (V/V) 1,2 PROPANEDIOL, 20% (V/V) PEG-400, 0.1 M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2012
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 45108 / % possible obs: 92.9 % / Observed criterion σ(I): 1.5 / Redundancy: 1.8 % / Biso Wilson estimate: 36.563 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.5 / % possible all: 92.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOWER RESOLUTION STRUCTURE OF CETZ

Resolution: 2→28.762 Å / SU ML: 0.28 / σ(F): 1.26 / Phase error: 26.26 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.229 3704 5 %
Rwork0.1821 --
obs0.1845 45065 77.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5531 0 56 185 5772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085663
X-RAY DIFFRACTIONf_angle_d1.2117623
X-RAY DIFFRACTIONf_dihedral_angle_d13.2072158
X-RAY DIFFRACTIONf_chiral_restr0.071858
X-RAY DIFFRACTIONf_plane_restr0.005976
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02630.35491360.3182640X-RAY DIFFRACTION75
2.0263-2.05410.38261300.31932602X-RAY DIFFRACTION75
2.0541-2.08340.38161340.31442613X-RAY DIFFRACTION74
2.0834-2.11450.33441290.30572467X-RAY DIFFRACTION70
2.1145-2.14750.31071350.27792685X-RAY DIFFRACTION76
2.1475-2.18270.33221270.25942751X-RAY DIFFRACTION79
2.1827-2.22040.26761260.25132834X-RAY DIFFRACTION80
2.2204-2.26070.28421280.24052739X-RAY DIFFRACTION78
2.2607-2.30420.27221540.23692757X-RAY DIFFRACTION79
2.3042-2.35120.28371750.22962783X-RAY DIFFRACTION79
2.3512-2.40230.32641650.23132701X-RAY DIFFRACTION78
2.4023-2.45810.25461430.21742725X-RAY DIFFRACTION77
2.4581-2.51960.25451350.20562668X-RAY DIFFRACTION76
2.5196-2.58770.24111140.19492471X-RAY DIFFRACTION70
2.5877-2.66380.28841440.20292763X-RAY DIFFRACTION79
2.6638-2.74970.24111480.18992850X-RAY DIFFRACTION81
2.7497-2.84790.2531330.19112821X-RAY DIFFRACTION80
2.8479-2.96180.27051550.19322823X-RAY DIFFRACTION80
2.9618-3.09640.25751490.18042726X-RAY DIFFRACTION79
3.0964-3.25950.25911700.18022666X-RAY DIFFRACTION77
3.2595-3.46340.21420.17232551X-RAY DIFFRACTION73
3.4634-3.73030.18481350.15732904X-RAY DIFFRACTION82
3.7303-4.10470.21061650.1482824X-RAY DIFFRACTION81
4.1047-4.69640.16961280.1332793X-RAY DIFFRACTION80
4.6964-5.90850.18621560.16842762X-RAY DIFFRACTION79
5.9085-28.7650.19021480.15182848X-RAY DIFFRACTION81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1751-0.2889-0.11030.76961.07572.91960.04360.0851-0.0475-0.2126-0.02540.0319-0.2415-0.0221-0.01620.1916-0.00170.00640.1495-0.01020.186619.158-5.6451-9.7933
21.7251-0.0678-0.41620.9605-0.06191.5573-0.2046-0.26750.15810.02110.13930.0146-0.1222-0.21560.02780.17330.0571-0.03460.1708-0.01720.20189.533913.520327.5676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

+
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