[English] 日本語
Yorodumi
- PDB-6mxw: Room-temperature structure of hydrogenated Tetdron (isomorph 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mxw
TitleRoom-temperature structure of hydrogenated Tetdron (isomorph 1)
ComponentsPhotoswitchable protein Tetdron
KeywordsFLUORESCENT PROTEIN / Tetdron / Photo-Switchable Protein / Beta-Barrel
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 2.049 Å
AuthorsDajnowicz, S. / Kovalevsky, A.
CitationJournal: To Be Published
Title: Room-temperature in crystallo photo-induced deprotonation and tetramerization of photo-switchable protein Padron2.0
Authors: Dajnowicz, S. / Langan, P.S. / Weiss, K.L. / Ivanov, I.N. / Kovalevsky, A.
History
DepositionOct 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Structure summary / Category: entity / struct / struct_keywords
Item: _entity.pdbx_description / _struct.pdbx_descriptor ..._entity.pdbx_description / _struct.pdbx_descriptor / _struct.title / _struct_keywords.text
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photoswitchable protein Tetdron
B: Photoswitchable protein Tetdron
C: Photoswitchable protein Tetdron
D: Photoswitchable protein Tetdron
E: Photoswitchable protein Tetdron
F: Photoswitchable protein Tetdron
G: Photoswitchable protein Tetdron
H: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)205,7778
Polymers205,7778
Non-polymers00
Water12,286682
1
A: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,7221
Polymers25,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,7221
Polymers25,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,7221
Polymers25,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,7221
Polymers25,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,7221
Polymers25,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,7221
Polymers25,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,7221
Polymers25,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Photoswitchable protein Tetdron


Theoretical massNumber of molelcules
Total (without water)25,7221
Polymers25,7221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.730, 129.966, 98.725
Angle α, β, γ (deg.)90.00, 105.32, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Photoswitchable protein Tetdron


Mass: 25722.186 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TLG6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 50 mM Tris pH 7.5, 0.15 M NaOAc, and 24% w/v polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 300 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.049→40 Å / Num. obs: 97428 / % possible obs: 96 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 74
Reflection shellResolution: 2.049→2.12 Å / Rmerge(I) obs: 0.344 / Num. unique obs: 4211

-
Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 2.049→35.995 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.28
RfactorNum. reflection% reflection
Rfree0.2009 4918 5.05 %
Rwork0.155 --
obs0.1574 97428 89.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.049→35.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13880 0 0 682 14562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714256
X-RAY DIFFRACTIONf_angle_d0.96719238
X-RAY DIFFRACTIONf_dihedral_angle_d17.8688386
X-RAY DIFFRACTIONf_chiral_restr0.0581962
X-RAY DIFFRACTIONf_plane_restr0.0052498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0491-2.07240.1994440.166707X-RAY DIFFRACTION21
2.0724-2.09680.2326680.17061355X-RAY DIFFRACTION39
2.0968-2.12230.22751030.18442118X-RAY DIFFRACTION61
2.1223-2.14920.22981220.18862551X-RAY DIFFRACTION74
2.1492-2.17750.21921520.18922981X-RAY DIFFRACTION86
2.1775-2.20730.24831850.18323185X-RAY DIFFRACTION93
2.2073-2.23880.26511820.1823299X-RAY DIFFRACTION95
2.2388-2.27220.22251610.17743323X-RAY DIFFRACTION97
2.2722-2.30770.22451800.17393370X-RAY DIFFRACTION98
2.3077-2.34560.26731770.16923397X-RAY DIFFRACTION98
2.3456-2.3860.22651830.16913408X-RAY DIFFRACTION98
2.386-2.42940.21561640.17273400X-RAY DIFFRACTION98
2.4294-2.47610.2311890.1763382X-RAY DIFFRACTION98
2.4761-2.52660.21821940.17123366X-RAY DIFFRACTION98
2.5266-2.58160.25741820.17573408X-RAY DIFFRACTION98
2.5816-2.64160.23091880.18083389X-RAY DIFFRACTION99
2.6416-2.70760.24431950.16523378X-RAY DIFFRACTION99
2.7076-2.78080.24351790.16043455X-RAY DIFFRACTION99
2.7808-2.86260.21861820.16063435X-RAY DIFFRACTION99
2.8626-2.9550.18881750.16773426X-RAY DIFFRACTION99
2.955-3.06050.21462040.17093383X-RAY DIFFRACTION99
3.0605-3.1830.20731830.16053431X-RAY DIFFRACTION98
3.183-3.32780.18221750.15453329X-RAY DIFFRACTION97
3.3278-3.50310.17641630.14283313X-RAY DIFFRACTION95
3.5031-3.72230.17061650.14113217X-RAY DIFFRACTION92
3.7223-4.00940.21441840.14053083X-RAY DIFFRACTION89
4.0094-4.41220.17631640.1342992X-RAY DIFFRACTION86
4.4122-5.04920.15261420.12172863X-RAY DIFFRACTION82
5.0492-6.35570.15731600.12853250X-RAY DIFFRACTION93
6.3557-36.00010.14961730.14183316X-RAY DIFFRACTION93

+
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