[English] 日本語
Yorodumi
- PDB-6gez: THE STRUCTURE OF TWITCH-2B N532F -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gez
TitleTHE STRUCTURE OF TWITCH-2B N532F
ComponentsGreen fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / TWITCH-2B / FRET / RATIOMETRIC BIOSENSOR
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / calcium ion binding
Similarity search - Function
Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
FORMIC ACID / Green fluorescent protein / Troponin C, skeletal muscle
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Opsanus tau (oyster toadfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsTrigo Mourino, P. / Paulat, M. / Thestrup, T. / Griesbeck, O. / Griesinger, C. / Becker, S.
Citation
Journal: Sci Adv / Year: 2019
Title: Dynamic tuning of FRET in a green fluorescent protein biosensor.
Authors: Trigo-Mourino, P. / Thestrup, T. / Griesbeck, O. / Griesinger, C. / Becker, S.
#1: Journal: Nat. Methods / Year: 2014
Title: Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes.
Authors: Thestrup, T. / Litzlbauer, J. / Bartholomaus, I. / Mues, M. / Russo, L. / Dana, H. / Kovalchuk, Y. / Liang, Y. / Kalamakis, G. / Laukat, Y. / Becker, S. / Witte, G. / Geiger, A. / Allen, T. ...Authors: Thestrup, T. / Litzlbauer, J. / Bartholomaus, I. / Mues, M. / Russo, L. / Dana, H. / Kovalchuk, Y. / Liang, Y. / Kalamakis, G. / Laukat, Y. / Becker, S. / Witte, G. / Geiger, A. / Allen, T. / Rome, L.C. / Chen, T.W. / Kim, D.S. / Garaschuk, O. / Griesinger, C. / Griesbeck, O.
History
DepositionApr 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
B: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,35611
Polymers124,9662
Non-polymers3909
Water1,40578
1
A: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7477
Polymers62,4831
Non-polymers2646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6094
Polymers62,4831
Non-polymers1263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.619, 157.472, 169.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein


Mass: 62482.961 Da / Num. of mol.: 2 / Mutation: N532F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Opsanus tau (oyster toadfish)
Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212, UniProt: W5IDB2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2 M SODIUM FORMIATE, PH 7.0, 5 MM CALCIUM CHLORIDE, 20 % PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→115.34 Å / Num. obs: 54945 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 6.36 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.95
Reflection shellResolution: 2.47→2.57 Å / Redundancy: 5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.95 / % possible all: 80.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GEL

6gel


Resolution: 2.47→115.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.885 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2736 5 %RANDOM
Rwork0.2067 ---
obs0.208 51921 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 144.05 Å2 / Biso mean: 72.324 Å2 / Biso min: 39.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2---0.15 Å20 Å2
3----2.37 Å2
Refinement stepCycle: final / Resolution: 2.47→115.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8531 0 19 78 8628
Biso mean--75.47 55.17 -
Num. residues----1067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198818
X-RAY DIFFRACTIONr_bond_other_d0.0050.028222
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.96911894
X-RAY DIFFRACTIONr_angle_other_deg1.249318993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.29851071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68425.278449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.871151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3941537
X-RAY DIFFRACTIONr_chiral_restr0.0910.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210073
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022028
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.472→2.536 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 147 -
Rwork0.378 2792 -
all-2939 -
obs--71.58 %
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)
10.72130.4848-0.06952.7943-0.27260.9234-0.03630.01740.1498-0.11280.06910.1069-0.03630.0535-0.03280.30130.0355-0.08680.0117-0.00880.0533-24.562-2.4682.953
20.48230.18291.10260.70380.25043.1075-0.0732-0.1479-0.06820.02810.0574-0.0786-0.0115-0.11660.01580.28690.16520.10540.20340.07850.1071-10.461-41.45837.393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 555
2X-RAY DIFFRACTION2B5 - 555

+
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