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- PDB-4xkb: Crystal Structure of GENOMES UNCOUPLED 4 (GUN4) in Complex with D... -

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Basic information

Entry
Database: PDB / ID: 4xkb
TitleCrystal Structure of GENOMES UNCOUPLED 4 (GUN4) in Complex with Deuteroporphyrin IX
ComponentsYcf53-like protein
KeywordsLIGAND BINDING PROTEIN / Gun4 / Deuteroporphyrin / Porphyrin-binding
Function / homology
Function and homology information


tetrapyrrole binding
Similarity search - Function
Gun4-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #620 / GUN4, N-terminal ARM-like repeat domain / ARM-like repeat domain, GUN4-N terminal / GUN4-like / GUN4-like superfamily / GUN4-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A ...Gun4-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #620 / GUN4, N-terminal ARM-like repeat domain / ARM-like repeat domain, GUN4-N terminal / GUN4-like / GUN4-like superfamily / GUN4-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-DE9 / Ycf53-like protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsChen, X. / Pu, H. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences2011CBA00901 China
CitationJournal: Mol Plant / Year: 2015
Title: Crystal Structures of GUN4 in Complex with Porphyrins.
Authors: Chen, X. / Pu, H. / Wang, X. / Long, W. / Lin, R. / Liu, L.
History
DepositionJan 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ycf53-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0012
Polymers26,4911
Non-polymers5111
Water6,287349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.792, 64.010, 105.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-DE9 / 3,3'-(3,7,12,17-tetramethylporphyrin-2,18-diyl)dipropanoic acid / deuteroporphyrin IX


Mass: 510.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: sodium cacodylate, sodium chloride, PEG 3350 / PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2014
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 36289 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 29.6
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y6I

1y6i


Resolution: 1.501→32.005 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1731 4.99 %
Rwork0.1603 34713 -
obs0.1621 34713 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→32.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1787 0 38 349 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061935
X-RAY DIFFRACTIONf_angle_d1.1452659
X-RAY DIFFRACTIONf_dihedral_angle_d13.44711
X-RAY DIFFRACTIONf_chiral_restr0.066279
X-RAY DIFFRACTIONf_plane_restr0.005343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5006-1.54480.2291920.17411782X-RAY DIFFRACTION63
1.5448-1.59470.23391300.17382488X-RAY DIFFRACTION88
1.5947-1.65170.21471280.16442807X-RAY DIFFRACTION98
1.6517-1.71780.21511520.15982838X-RAY DIFFRACTION100
1.7178-1.79590.19451460.1542846X-RAY DIFFRACTION100
1.7959-1.89060.19761660.14612839X-RAY DIFFRACTION100
1.8906-2.00910.18291670.13952834X-RAY DIFFRACTION100
2.0091-2.16420.16931550.14252878X-RAY DIFFRACTION100
2.1642-2.38190.19881450.14922882X-RAY DIFFRACTION100
2.3819-2.72640.19731490.16192903X-RAY DIFFRACTION100
2.7264-3.43430.19831360.17112953X-RAY DIFFRACTION100
3.4343-32.01230.19431650.17032932X-RAY DIFFRACTION95

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