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- PDB-7e2s: Synechocystis GUN4 in complex with biliverdin IXa -

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Basic information

Entry
Database: PDB / ID: 7e2s
TitleSynechocystis GUN4 in complex with biliverdin IXa
ComponentsYcf53-like protein
KeywordsSIGNALING PROTEIN / GUN4 / LIGAND BINDING PROTEIN
Function / homologyGUN4, N-terminal ARM-like repeat domain / ARM-like repeat domain, GUN4-N terminal / GUN4-like / GUN4-like superfamily / GUN4-like / tetrapyrrole binding / Armadillo-type fold / BILIVERDINE IX ALPHA / Ycf53-like protein
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ycf53-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2584
Polymers26,4911
Non-polymers7673
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-9 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.497, 64.449, 106.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ycf53-like protein / GUN4


Mass: 26490.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll0558 / Production host: Escherichia coli (E. coli) / References: UniProt: P72583
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: HEPES pH 7.0, Jeffamine M-600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 105355 / % possible obs: 99.8 % / Redundancy: 12 % / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.027 / Net I/σ(I): 23.2
Reflection shellResolution: 1.05→1.09 Å / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 10208 / CC1/2: 0.916 / Rpim(I) all: 0.158

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XKB

4xkb


Resolution: 1.05→41.13 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 11.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1343 5096 5.03 %
Rwork0.1177 96144 -
obs0.1185 101240 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.19 Å2 / Biso mean: 20.6295 Å2 / Biso min: 10.4 Å2
Refinement stepCycle: final / Resolution: 1.05→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 100 416 2386
Biso mean--29.77 34.58 -
Num. residues----233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.05-1.060.3089930.3089183956
1.06-1.070.251210.2398236871
1.07-1.090.19541220.1794262179
1.09-1.10.15861520.1574287087
1.1-1.120.17471600.1418307992
1.12-1.130.14591730.1296314096
1.13-1.150.13951780.1263321197
1.15-1.160.15191820.1203327999
1.16-1.180.1421700.1186325399
1.18-1.20.14732040.11373309100
1.2-1.220.12041750.113256100
1.22-1.250.13461870.1113313100
1.25-1.270.12281960.1123277100
1.27-1.290.14071630.11383325100
1.29-1.320.15481780.11523305100
1.32-1.350.1381790.11663352100
1.35-1.390.14431850.113302100
1.39-1.430.13961490.10783344100
1.43-1.470.141890.10423337100
1.47-1.510.12641490.10233330100
1.51-1.570.12861810.10313351100
1.57-1.630.13161820.10463357100
1.63-1.710.12681630.10733350100
1.71-1.80.1261710.11413375100
1.8-1.910.13671800.11513371100
1.91-2.060.13591850.11423341100
2.06-2.260.12161830.11083382100
2.26-2.590.12611750.11553431100
2.59-3.260.14581940.12183447100
3.26-41.130.13011770.12533629100

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