[English] 日本語
Yorodumi
- PDB-8zbo: Crystal structure of the biphotochromic fluorescent protein moxSA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zbo
TitleCrystal structure of the biphotochromic fluorescent protein moxSAASoti (F97M variant) in its green on-state
ComponentsF97M variant of the biphotochromic fluorescent protein moxSAASoti
KeywordsFLUORESCENT PROTEIN / moxSAASoti / point mutant / chromophore / mSAASoti / SAASoti / biphotochromic
Function / homologyNITRATE ION / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesStylocoeniella armata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBoyko, K.M. / Matyuta, I.O. / Marynich, N.K. / Minyaev, M.E. / Khadiyatova, A.A. / Popov, V.O. / Savitsky, A.P.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Single-point substitution F97M leads to in cellulo crystallization of the biphotochromic protein moxSAASoti.
Authors: Marynich, N.K. / Boyko, K.M. / Matyuta, I.O. / Minyaev, M.E. / Khadiyatova, A.A. / Popov, V.O. / Savitsky, A.P.
History
DepositionApr 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Nov 13, 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
C: F97M variant of the biphotochromic fluorescent protein moxSAASoti
A: F97M variant of the biphotochromic fluorescent protein moxSAASoti
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,00111
Polymers50,3552
Non-polymers6469
Water4,414245
1
C: F97M variant of the biphotochromic fluorescent protein moxSAASoti
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5507
Polymers25,1781
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area9320 Å2
MethodPISA
2
A: F97M variant of the biphotochromic fluorescent protein moxSAASoti
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4524
Polymers25,1781
Non-polymers2743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint1 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.652, 81.254, 98.813
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein F97M variant of the biphotochromic fluorescent protein moxSAASoti


Mass: 25177.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stylocoeniella armata (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium nitrate hexahydrate, 20% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Nov 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→21.83 Å / Num. obs: 29554 / % possible obs: 99 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.026 / Rrim(I) all: 0.086 / Χ2: 1.17 / Net I/σ(I): 27.3 / Num. measured all: 325806
Reflection shellResolution: 2→2.05 Å / % possible obs: 98 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.449 / Num. measured all: 23609 / Num. unique obs: 2110 / CC1/2: 0.954 / Rpim(I) all: 0.138 / Rrim(I) all: 0.47 / Χ2: 0.87 / Net I/σ(I) obs: 5.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 7.616 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23107 1475 5 %RANDOM
Rwork0.17764 ---
obs0.18041 27773 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.436 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2---0.33 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: 1 / Resolution: 2→21.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 42 245 3608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123503
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163177
X-RAY DIFFRACTIONr_angle_refined_deg2.261.8334714
X-RAY DIFFRACTIONr_angle_other_deg0.8841.7637366
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4665412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.103527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48210582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.024022
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02796
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_it2.0761.5251663
X-RAY DIFFRACTIONr_mcbond_other2.0761.5261663
X-RAY DIFFRACTIONr_mcangle_it2.9482.7212063
X-RAY DIFFRACTIONr_mcangle_other2.9482.7212064
X-RAY DIFFRACTIONr_scbond_it3.0761.8981840
X-RAY DIFFRACTIONr_scbond_other3.0761.8991841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5013.3142651
X-RAY DIFFRACTIONr_long_range_B_refined6.5717.793743
X-RAY DIFFRACTIONr_long_range_B_other6.56917.793744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 103 -
Rwork0.201 1977 -
obs--97.47 %
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)
11.37930.41190.25382.0810.2611.91940.00410.0052-0.11750.0338-0.0051-0.10960.12740.11670.0010.01250.0050.00410.0092-0.0010.017-4.188212.5092-14.6154
21.55940.6341-0.04742.0753-0.52671.9610.0126-0.0720.25310.2137-0.0550.1376-0.2871-0.10220.04240.05840.0109-0.00630.0246-0.00870.051910.080842.7526-8.3062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C7 - 221
2X-RAY DIFFRACTION2A8 - 219

+
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