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- PDB-7e2r: The ligand-free structure of Arabidopsis thaliana GUN4 -

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Basic information

Entry
Database: PDB / ID: 7e2r
TitleThe ligand-free structure of Arabidopsis thaliana GUN4
ComponentsTetrapyrrole-binding protein, chloroplastic
KeywordsSIGNALING PROTEIN / GUN4 / LIGAND BINDING PROTEIN
Function / homology
Function and homology information


chloroplast-nucleus signaling pathway / chloroplast membrane / chlorophyll biosynthetic process / tetrapyrrole binding / positive regulation of catalytic activity / chloroplast / enzyme binding
Similarity search - Function
GUN4-like / GUN4-like superfamily / GUN4-like
Similarity search - Domain/homology
Tetrapyrrole-binding protein, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLiu, L. / Hu, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503703 China
CitationJournal: Protein Sci. / Year: 2021
Title: Structural basis of bilin binding by the chlorophyll biosynthesis regulator GUN4.
Authors: Hu, J.H. / Chang, J.W. / Xu, T. / Wang, J. / Wang, X. / Lin, R. / Duanmu, D. / Liu, L.
History
DepositionFeb 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetrapyrrole-binding protein, chloroplastic
B: Tetrapyrrole-binding protein, chloroplastic


Theoretical massNumber of molelcules
Total (without water)47,2512
Polymers47,2512
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-12 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.758, 64.118, 55.705
Angle α, β, γ (deg.)90.000, 91.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 78 through 94 or resid 96 through 227))
21(chain B and (resid 78 through 94 or resid 96 through 174 or resid 184 through 227))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARG(chain A and (resid 78 through 94 or resid 96 through 227))AA78 - 9410 - 26
12ALAALATHRTHR(chain A and (resid 78 through 94 or resid 96 through 227))AA96 - 22728 - 159
21ALAALAARGARG(chain B and (resid 78 through 94 or resid 96 through 174 or resid 184 through 227))BB78 - 9410 - 26
22ALAALALEULEU(chain B and (resid 78 through 94 or resid 96 through 174 or resid 184 through 227))BB96 - 17428 - 106
23TYRTYRTHRTHR(chain B and (resid 78 through 94 or resid 96 through 174 or resid 184 through 227))BB184 - 227116 - 159

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Components

#1: Protein Tetrapyrrole-binding protein, chloroplastic / Genomes uncoupled 4


Mass: 23625.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GUN4, At3g59400, F25L23_260 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LX31
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 1.8 Å3/Da / Density % sol: 31.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris, Polythylene glycol monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15049 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.084 / Net I/σ(I): 9
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.813 / Num. unique obs: 1495 / CC1/2: 0.651 / Rpim(I) all: 0.486 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xkb

4xkb


Resolution: 2.3→42.04 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 691 4.6 %
Rwork0.1946 14318 -
obs0.1961 15009 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.68 Å2 / Biso mean: 32.5839 Å2 / Biso min: 16.52 Å2
Refinement stepCycle: final / Resolution: 2.3→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 0 178 2576
Biso mean---36.1 -
Num. residues----290
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1350X-RAY DIFFRACTION12.566TORSIONAL
12B1350X-RAY DIFFRACTION12.566TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.480.32251430.262528362979100
2.48-2.730.2921360.25392816295299
2.73-3.120.25431310.218728813012100
3.12-3.930.23351440.180328593003100
3.93-42.040.1581370.157529263063100
Refinement TLS params.Method: refined / Origin x: 31.6766 Å / Origin y: 27.4056 Å / Origin z: 43.7851 Å
111213212223313233
T0.1888 Å2-0.0374 Å20.0019 Å2-0.2136 Å20.0022 Å2--0.2212 Å2
L1.1203 °2-0.4097 °2-0.0117 °2-0.7398 °2-0.422 °2--2.1848 °2
S0.013 Å °-0.1469 Å °0.0034 Å °-0.0344 Å °-0.0399 Å °-0.0166 Å °-0.0566 Å °0.3675 Å °0.0161 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA78 - 227
2X-RAY DIFFRACTION1allB73 - 227
3X-RAY DIFFRACTION1allS1 - 181

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