[English] 日本語
Yorodumi
- PDB-6aa2: X-ray structure of ReQy1 (oxidized form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aa2
TitleX-ray structure of ReQy1 (oxidized form)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / redox status / fluorescent indicator protein / YFP
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSugiura, K. / Yasuda, A. / Tabushi, N. / Tanaka, H. / Kurisu, G. / Hisabori, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and TechnologyCREST Japan
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Multicolor redox sensor proteins can visualize redox changes in various compartments of the living cell.
Authors: Sugiura, K. / Tanaka, H. / Kurisu, G. / Wakabayashi, K.I. / Hisabori, T.
History
DepositionJul 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: 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: Green fluorescent protein
B: Green fluorescent protein
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)85,1763
Polymers85,1763
Non-polymers00
Water6,990388
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,3921
Polymers28,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,3921
Polymers28,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,3921
Polymers28,3921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.571, 120.520, 115.028
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23B
14A
24C
15B
25C
16B
26C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 64
2010B5 - 64
1020A5 - 64
2020C5 - 64
1030A68 - 229
2030B68 - 229
1040A68 - 229
2040C68 - 229
1050B5 - 64
2050C5 - 64
1060B68 - 240
2060C68 - 240

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein Green fluorescent protein


Mass: 28392.043 Da / Num. of mol.: 3
Mutation: K26R, F46L, T65G, S72A, R80Q, S99F, Y145G, N146W, S147CA, V150I, T167I, T203Y, Q204C, H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE SER 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE CR2 65.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM Tris-HCl(pH 7.5), 150mM NaCl, 250mM Trilithium Citrate, 14%(w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 43945 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 33.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.457 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MYW

1myw


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.386 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22859 2104 4.8 %RANDOM
Rwork0.18374 ---
obs0.18582 41814 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.555 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20.17 Å2
2--0.07 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5520 0 0 390 5910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195657
X-RAY DIFFRACTIONr_bond_other_d0.0020.025135
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9657642
X-RAY DIFFRACTIONr_angle_other_deg1311956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2985683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12424.982273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48615957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8011521
X-RAY DIFFRACTIONr_chiral_restr0.1130.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216277
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021132
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7124.0052750
X-RAY DIFFRACTIONr_mcbond_other3.7094.0042749
X-RAY DIFFRACTIONr_mcangle_it5.2975.9993427
X-RAY DIFFRACTIONr_mcangle_other5.2965.9993428
X-RAY DIFFRACTIONr_scbond_it5.0724.5062906
X-RAY DIFFRACTIONr_scbond_other5.0714.5062907
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8556.5294216
X-RAY DIFFRACTIONr_long_range_B_refined9.7345.9525919
X-RAY DIFFRACTIONr_long_range_B_other9.70345.7755853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A31060.06
12B31060.06
21A31380.05
22C31380.05
31A97480.09
32B97480.09
41A97680.08
42C97680.08
51B31140.05
52C31140.05
61B104660.07
62C104660.07
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 148 -
Rwork0.286 2980 -
obs--95.95 %

+
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