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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7djl
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 / Haloacid dehalogenase-like hydrolase / Thioredoxin-like / NHL repeat / NHL repeat / Haloacid dehalogenase-like hydrolase / Thioredoxin-like fold / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Phosphoglycolate phosphatase-like, domain 2 ...NHL2, NHL repeat domain / Haloacid dehalogenase-like hydrolase / Thioredoxin-like / NHL repeat / NHL repeat / Haloacid dehalogenase-like hydrolase / Thioredoxin-like fold / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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
Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.96077824385 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
C: Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
A: Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
B: Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,4656
Polymers162,3713
Non-polymers943
Water95553
1
C: Protein SUPPRESSOR OF QUENCHING 1, chloroplastic


Theoretical massNumber of molelcules
Total (without water)54,1241
Polymers54,1241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20490 Å2
MethodPISA
2
A: Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1943
Polymers54,1241
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-13 kcal/mol
Surface area20610 Å2
MethodPISA
3
B: Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1472
Polymers54,1241
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.933, 166.298, 95.740
Angle α, β, γ (deg.)90.000, 116.824, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Protein SUPPRESSOR OF QUENCHING 1, chloroplastic


Mass: 54123.543 Da / Num. of mol.: 3 / Fragment: NHL-CTD / Mutation: E859K
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 25% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M MES, pH 5.3

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 43808 / % possible obs: 98.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 65.1490505897 Å2 / Rrim(I) all: 0.114 / Net I/σ(I): 13.86
Reflection shellResolution: 2.95→3 Å / Num. unique obs: 2195 / CC1/2: 0.78

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GCI

6gci


Resolution: 2.96077824385→44.5984906764 Å / SU ML: 0.336572799659 / Cross valid method: FREE R-VALUE / σ(F): 1.34753457772 / Phase error: 25.8798813777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22622644028 2131 4.86440832725 %
Rwork0.168459538606 41677 -
obs0.171264525779 43808 98.0022818281 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.5710276364 Å2
Refinement stepCycle: LAST / Resolution: 2.96077824385→44.5984906764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10834 0 3 53 10890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010959265878811113
X-RAY DIFFRACTIONf_angle_d1.2937569991215067
X-RAY DIFFRACTIONf_chiral_restr0.07639967752741693
X-RAY DIFFRACTIONf_plane_restr0.01077855349881993
X-RAY DIFFRACTIONf_dihedral_angle_d20.62451486944106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9608-3.02960.3203939718091330.2424649404762670X-RAY DIFFRACTION95.1782682513
3.0296-3.10540.3326931658371710.2252320703272791X-RAY DIFFRACTION99.4293387043
3.1054-3.18930.283034466581410.2239919645162825X-RAY DIFFRACTION99.1973244147
3.1893-3.28310.3249472083861390.2204731245392776X-RAY DIFFRACTION99.2171545269
3.2831-3.38910.271275512691530.2057355297272808X-RAY DIFFRACTION99.1959798995
3.3891-3.51020.3028611224811450.2160519009182741X-RAY DIFFRACTION97.1717171717
3.5102-3.65060.2616150580081410.1874845863052707X-RAY DIFFRACTION95.5384099296
3.6506-3.81670.2371567198691310.1902271078112759X-RAY DIFFRACTION97.6021614319
3.8167-4.01780.2428102073451390.1805147404092783X-RAY DIFFRACTION97.9879275654
4.0178-4.26930.2156036066011280.1349914027162825X-RAY DIFFRACTION99.2271505376
4.2693-4.59870.1650455314251490.1206762511562789X-RAY DIFFRACTION98.6236992279
4.5987-5.06090.1628416946241250.1196272500942790X-RAY DIFFRACTION98.0491086445
5.0609-5.79190.2168001349431360.1436420241912755X-RAY DIFFRACTION96.5275459098
5.7919-7.2920.244299495041550.1783393505472829X-RAY DIFFRACTION99.4998332778
7.292-44.59849067640.170893826861450.1698061012312829X-RAY DIFFRACTION97.6042008533
Refinement TLS params.Method: refined / Origin x: 181.92177557 Å / Origin y: -11.026169049 Å / Origin z: 15.9441565202 Å
111213212223313233
T0.556506246738 Å20.00388768215468 Å2-0.0256584649635 Å2-0.50445419847 Å20.00051915493815 Å2--0.524033777597 Å2
L0.347788900144 °20.0601065665972 °2-0.15663928714 °2-0.149517853422 °20.0301135265793 °2--0.48537464558 °2
S0.0222714786241 Å °0.0248480867163 Å °-0.00878549797976 Å °-0.0295193946025 Å °-0.0224065438334 Å °0.0323953231947 Å °-0.0459671102028 Å °-0.0674800332412 Å °-0.0043991435896 Å °
Refinement TLS groupSelection details: all

+
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