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- PDB-7e2t: Synechocystis GUN4 in complex with phycocyanobilin -

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Basic information

Entry
Database: PDB / ID: 7e2t
TitleSynechocystis GUN4 in complex with phycocyanobilin
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 / Chem-UYC / Ycf53-like protein
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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)27,1133
Polymers26,4911
Non-polymers6222
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-10 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.465, 64.695, 106.521
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-UYC / 3-[2-[(~{Z})-[5-[(~{Z})-[(4~{R})-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 586.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 41.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: Sodium citrate pH 5.5, PEG 6000

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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: Sep 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 91915 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.05 / Net I/σ(I): 15.5
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9050 / CC1/2: 0.838 / Rpim(I) all: 0.27 / % possible all: 100

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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: 4XKC

4xkc


Resolution: 1.1→30.95 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1563 3786 4.89 %
Rwork0.1252 73635 -
obs0.1267 77421 84.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.28 Å2 / Biso mean: 23.8522 Å2 / Biso min: 12.57 Å2
Refinement stepCycle: final / Resolution: 1.1→30.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 80 387 2312
Biso mean--32.64 39.25 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.110.2837100.37532212317
1.11-1.130.5021280.320455558318
1.13-1.140.3334410.2867963100430
1.14-1.160.3296770.25651413149044
1.16-1.180.2372810.2211845192658
1.18-1.20.2245950.20272334242972
1.2-1.220.24851440.1792627277183
1.22-1.240.22171540.17042816297089
1.24-1.260.22251450.17232944308991
1.26-1.280.20831470.1723026317394
1.28-1.310.18611540.16993065321995
1.31-1.340.17021690.15763072324196
1.34-1.370.21641440.16163126327097
1.37-1.40.18541800.1583187336799
1.4-1.440.16791620.14243163332599
1.44-1.480.17541520.134332583410100
1.48-1.530.17391890.132631653354100
1.53-1.590.15661780.127332073385100
1.59-1.650.1641790.122732313410100
1.65-1.730.16581750.126632323407100
1.73-1.820.16541710.123632463417100
1.82-1.930.16761540.118932603414100
1.93-2.080.13111700.115532533423100
2.08-2.290.14581680.111532853453100
2.29-2.620.14431790.113232943473100
2.62-3.30.15331630.118933543517100
3.3-30.950.14271770.120734933670100

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