[English] 日本語
Yorodumi
- PDB-6aa6: X-ray structure of ReQy1 (reduced form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aa6
TitleX-ray structure of ReQy1 (reduced form)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / YFP / fluorescent indicator protein / redox
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: 2.39 Å
AuthorsKurisu, G. / Yasuda, A. / Tabushi, N. / Tanaka, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)A16H065600 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)56,7522
Polymers56,7522
Non-polymers00
Water3,909217
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,3761
Polymers28,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,3761
Polymers28,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.009, 70.562, 65.069
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUAA4 - 648 - 68
21GLYGLYLEULEUBB4 - 648 - 68
12VALVALGLYGLYAA68 - 22870 - 231
22VALVALGLYGLYBB68 - 22870 - 231

NCS ensembles :
ID
1
2

-
Components

#1: Protein Green fluorescent protein / ReQy1


Mass: 28375.980 Da / Num. of mol.: 2
Mutation: K26R, F46L, T65G, S72A, R80Q, S99F, Y145G, N146W, S147SA, 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.: 217 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50mM Tris-HCl(pH7.0), 150mM NaCl, 20%(w/v) PEG3350

-
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: 2.4→64.84 Å / Num. obs: 20231 / % possible obs: 95.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 13.7
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.572 / % possible all: 97.5

-
Processing

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

1myw


Resolution: 2.39→64.84 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.922 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24729 1089 5.4 %RANDOM
Rwork0.19004 ---
obs0.19318 19126 95.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.02 Å2
2--0 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.39→64.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 0 217 3899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193774
X-RAY DIFFRACTIONr_bond_other_d0.0020.023409
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9625097
X-RAY DIFFRACTIONr_angle_other_deg0.96237939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8555456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17824.946184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5815634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4171514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214200
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02758
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_it2.2543.1341836
X-RAY DIFFRACTIONr_mcbond_other2.2493.1331835
X-RAY DIFFRACTIONr_mcangle_it3.5484.6952288
X-RAY DIFFRACTIONr_mcangle_other3.5474.6972289
X-RAY DIFFRACTIONr_scbond_it2.6743.3841938
X-RAY DIFFRACTIONr_scbond_other2.6743.3851939
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.384.9442810
X-RAY DIFFRACTIONr_long_range_B_refined6.2435.4934033
X-RAY DIFFRACTIONr_long_range_B_other6.21635.4914003
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)
11A30980.09
12B30980.09
21A96360.1
22B96360.1
LS refinement shellResolution: 2.392→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 87 -
Rwork0.292 1354 -
obs--92.61 %

+
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