[English] 日本語
Yorodumi
- PDB-7djm: Structure of four truncated and mutated forms of quenching protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7djm
TitleStructure of four truncated and mutated forms of quenching protein
ComponentsProtein SUPPRESSOR OF QUENCHING 1, chloroplastic
KeywordsPLANT PROTEIN / Suppressor / Quenching
Function / homology
Function and homology information


nonphotochemical quenching / thylakoid membrane / chloroplast thylakoid / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / hydrolase activity / metal ion binding / nucleus
Similarity search - Function
NHL2, NHL repeat domain / Thioredoxin-like / NHL repeat / NHL repeat / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Thioredoxin-like fold / Phosphoglycolate phosphatase-like, domain 2 ...NHL2, NHL repeat domain / Thioredoxin-like / NHL repeat / NHL repeat / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Thioredoxin-like fold / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Six-bladed beta-propeller, TolB-like / Thioredoxin domain profile. / Thioredoxin domain / HAD superfamily / HAD-like superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
ACETATE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.70000117792 Å
AuthorsYu, G.M. / Pan, X.W. / Li, M.
Funding support China, 6items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0502900 China
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)31600609 China
National Natural Science Foundation of China (NSFC)31770778 China
Chinese Academy of Sciences2018128 China
CitationJournal: Nat.Plants / Year: 2022
Title: Structure of Arabidopsis SOQ1 lumenal region unveils C-terminal domain essential for negative regulation of photoprotective qH.
Authors: Yu, G. / Hao, J. / Pan, X. / Shi, L. / Zhang, Y. / Wang, J. / Fan, H. / Xiao, Y. / Yang, F. / Lou, J. / Chang, W. / Malnoe, A. / Li, M.
History
DepositionNov 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4195
Polymers54,1231
Non-polymers2954
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-17 kcal/mol
Surface area19650 Å2
Unit cell
Length a, b, c (Å)55.000, 78.750, 103.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Protein SUPPRESSOR OF QUENCHING 1, chloroplastic


Mass: 54123.477 Da / Num. of mol.: 1 / Fragment: NHL_CTD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOQ1, At1g56500, F13N6.21 / Production host: Komagataella phaffii GS115 (fungus)
References: UniProt: Q8VZ10, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 25-34% PEG 3350, 0.2 M NH4Ac, 0.1M MES, pH 5.9-6.6 / PH range: 5.9-6.6

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9777 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 49848 / % possible obs: 99.8 % / Redundancy: 12.4 % / Biso Wilson estimate: 22.0080859116 Å2 / Rrim(I) all: 0.082 / Net I/σ(I): 33.36
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 2367 / CC1/2: 0.864

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DJJ

7djj


Resolution: 1.70000117792→39.375 Å / SU ML: 0.167139620693 / Cross valid method: FREE R-VALUE / σ(F): 1.36333929852 / Phase error: 19.4162754482
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.211328545844 2507 5.02928903868 %
Rwork0.18628968042 47341 -
obs0.187504658017 49848 99.7199327839 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.9819224725 Å2
Refinement stepCycle: LAST / Resolution: 1.70000117792→39.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3492 0 17 284 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009040219639043598
X-RAY DIFFRACTIONf_angle_d1.01458728324874
X-RAY DIFFRACTIONf_chiral_restr0.0783583965909548
X-RAY DIFFRACTIONf_plane_restr0.00696203604645
X-RAY DIFFRACTIONf_dihedral_angle_d19.22045247051326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.70000117792-1.73270.2778696675771600.248286115032483X-RAY DIFFRACTION96.1440523827
1.7000012-4.45320.2194871974621370.207609183652824X-RAY DIFFRACTION98.9969909729
1.7327-1.76810.2445362110831480.2247685096912577X-RAY DIFFRACTION99.9633162142
1.7681-1.80650.2229886653881540.2106918583862587X-RAY DIFFRACTION100
1.8065-1.84850.1958415944221270.15512625X-RAY DIFFRACTION99.9636759898
1.8485-1.89480.2208245642131330.1918733923372601X-RAY DIFFRACTION100
1.8948-1.9460.2535079197861230.1973449092792619X-RAY DIFFRACTION100
1.946-2.00320.2080938793151500.1887199963842587X-RAY DIFFRACTION100
2.0032-2.06790.225067775871420.188159760572615X-RAY DIFFRACTION100
2.0679-2.14180.2106951465711420.1806567098922605X-RAY DIFFRACTION100
2.1418-2.22760.1995856242181510.1837563620532609X-RAY DIFFRACTION99.9637812387
2.2276-2.32890.1955501880421310.1862666784162629X-RAY DIFFRACTION100
2.3289-2.45170.1983872374131320.1812312289792649X-RAY DIFFRACTION100
2.4517-2.60530.2291451739681550.187296576832623X-RAY DIFFRACTION100
2.6053-2.80640.2375689725541230.1910864376622656X-RAY DIFFRACTION100
2.8064-3.08870.2358245849081310.1860223114822673X-RAY DIFFRACTION100
3.0887-3.53540.2099450453191190.1778931705282686X-RAY DIFFRACTION99.9643620813
3.5354-4.45320.1726150767181490.1550832277562693X-RAY DIFFRACTION100

+
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