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- PDB-1y6i: Synechocystis GUN4 -

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Basic information

Entry
Database: PDB / ID: 1y6i
TitleSynechocystis GUN4
ComponentsMg-chelatase cofactor GUN4
KeywordsLIGAND BINDING PROTEIN / Helix-Bundle / 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
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.78 Å
AuthorsVerdecia, M.A. / Larkin, R.M. / Ferrer, J.L. / Riek, R. / Chory, J. / Noel, J.P.
CitationJournal: Plos Biol. / Year: 2005
Title: Structure of the Mg-chelatase cofactor GUN4 reveals a novel hand-shaped fold for porphyrin binding
Authors: Verdecia, M.A. / Larkin, R.M. / Ferrer, J.L. / Riek, R. / Chory, J. / Noel, J.P.
History
DepositionDec 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mg-chelatase cofactor GUN4


Theoretical massNumber of molelcules
Total (without water)26,4911
Polymers26,4911
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.907, 70.710, 72.645
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 Mg-chelatase cofactor GUN4


Mass: 26490.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: gun4 / Plasmid: pHIS8-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P72583
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, NaBr, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE
DetectorType: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Jun 15, 2003 / Details: mirrors
RadiationMonochromator: Pt/Ni Coated Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.78→48 Å / Num. obs: 17157 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 21.8 Å2
Reflection shellHighest resolution: 1.78 Å / Mean I/σ(I) obs: 15.8 / Num. unique all: 58495

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.78→32.31 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1165268.53 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1594 5 %RANDOM
Rwork0.221 ---
obs0.221 17157 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9461 Å2 / ksol: 0.348501 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--4.96 Å20 Å2
3----3.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.78→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 0 249 2125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 256 5 %
Rwork0.334 4857 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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