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- PDB-6ysg: Magnesium chelatase H subunit (ChlH) from Synechocystis sp.PCC680... -

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Basic information

Entry
Database: PDB / ID: 6ysg
TitleMagnesium chelatase H subunit (ChlH) from Synechocystis sp.PCC6803 to 2.54 A resolution
ComponentsMg-chelatase subunit ChlH
KeywordsPHOTOSYNTHESIS / Magnesium chelatase / chlorophyll
Function / homology
Function and homology information


magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / ATP binding
Similarity search - Function
Magnesium-chelatase, subunit H / Magnesium chelatase, subunit H, N-terminal / Domain of unknown function (DUF3479) / CobN/magnesium chelatase / CobN/Magnesium Chelatase
Similarity search - Domain/homology
CITRIC ACID / magnesium chelatase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsBisson, C. / Hunter, C.N.
Funding support1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)
CitationJournal: Nat.Plants / Year: 2020
Title: The active site of magnesium chelatase.
Authors: Adams, N.B.P. / Bisson, C. / Brindley, A.A. / Farmer, D.A. / Davison, P.A. / Reid, J.D. / Hunter, C.N.
History
DepositionApr 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: 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 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mg-chelatase subunit ChlH
B: Mg-chelatase subunit ChlH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,9353
Polymers301,7432
Non-polymers1921
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel permeation chromatography in an FPLC system
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-9 kcal/mol
Surface area92480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)321.119, 321.119, 104.966
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Mg-chelatase subunit ChlH


Mass: 150871.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Gene: chlH / Production host: Escherichia coli (E. coli) / References: UniProt: P73020
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8-1.2M Sodium citrate pH7.0 and 2 mM dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98674 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98674 Å / Relative weight: 1
ReflectionResolution: 2.54→83.78 Å / Num. obs: 133090 / % possible obs: 100 % / Redundancy: 8.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.041 / Rrim(I) all: 0.12 / Net I/σ(I): 12.1 / Num. measured all: 1143007 / Scaling rejects: 509
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.54-2.748.31.341227759274610.6380.4951.4311.7
6.72-83.788.70.0326274271810.9990.0120.03438.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHJ

4zhj


Resolution: 2.54→83.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.297 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 6684 5 %RANDOM
Rwork0.2019 ---
obs0.2046 125966 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 177.89 Å2 / Biso mean: 58.372 Å2 / Biso min: 22.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----2.61 Å2
Refinement stepCycle: final / Resolution: 2.54→83.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19596 0 13 114 19723
Biso mean--93.45 38.82 -
Num. residues----2489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01320003
X-RAY DIFFRACTIONr_bond_other_d0.0020.01718488
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.63927123
X-RAY DIFFRACTIONr_angle_other_deg1.2961.57142961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40152471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60423.1951083
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.406153433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.11715122
X-RAY DIFFRACTIONr_chiral_restr0.070.22574
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024026
LS refinement shellResolution: 2.54→2.606 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 504 -
Rwork0.368 9192 -
all-9696 -
obs--98.76 %

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