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- PDB-7djj: Structure of four truncated and mutated forms of quenching protei... -

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Basic information

Entry
Database: PDB / ID: 7djj
TitleStructure of four truncated and mutated forms of quenching protein lumenal domains
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
Protein SUPPRESSOR OF QUENCHING 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69806436563 Å
AuthorsYu, G.M. / Pan, X.W. / Li, M.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31600609 China
National Natural Science Foundation of China (NSFC)31770778 China
Chinese Academy of SciencesXDB27020106 China
Chinese Academy of Sciences2018128 China
Ministry of Science and Technology (MoST, China)2016YFA0502900 China
Ministry of Science and Technology (MoST, China)2017YFA0503702 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,3913
Polymers73,2721
Non-polymers1192
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint-30 kcal/mol
Surface area14070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.540, 80.540, 172.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Protein SUPPRESSOR OF QUENCHING 1, chloroplastic


Mass: 73272.367 Da / Num. of mol.: 1 / Fragment: NHL domain
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 1.2 M NaH2PO4, 0.8 MK2HPO4, 0.2 M Li2SO4. 0.1 M Capso, pH 9.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.69806436563→50 Å / Num. obs: 16265 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 54.2982342093 Å2 / Rpim(I) all: 0.031 / Net I/σ(I): 24.75
Reflection shellResolution: 2.69806436563→2.75 Å / Num. unique obs: 792 / CC1/2: 0.957 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.69806436563→47.519704511 Å / SU ML: 0.266161352112 / Cross valid method: FREE R-VALUE / σ(F): 1.34350293645 / Phase error: 26.2325478047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233744942523 812 4.99231478635 %
Rwork0.193887041726 15453 -
obs0.195938430209 16265 99.5775682625 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.685119756 Å2
Refinement stepCycle: LAST / Resolution: 2.69806436563→47.519704511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 6 26 2717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01128318918892739
X-RAY DIFFRACTIONf_angle_d1.323041281413711
X-RAY DIFFRACTIONf_chiral_restr0.0719387817459408
X-RAY DIFFRACTIONf_plane_restr0.0114962628001497
X-RAY DIFFRACTIONf_dihedral_angle_d14.23328500591634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6981-2.86710.3506056260571230.2511283523392505X-RAY DIFFRACTION99.2072480181
2.8671-3.08840.3026634376061250.2508414620272533X-RAY DIFFRACTION99.6251874063
3.0884-3.39910.2787713687011250.2241144926352535X-RAY DIFFRACTION99.7375328084
3.3991-3.89080.2208242224041510.1947537172432537X-RAY DIFFRACTION99.7402597403
3.8908-4.90120.193309892571430.1546090853852598X-RAY DIFFRACTION99.8179169701
4.9012-47.5190.2312843240041450.1918825443042745X-RAY DIFFRACTION99.3468545892

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