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- PDB-6yt0: Magnesium chelatase H subunit (ChlH) E660D variant from Synechocy... -

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Basic information

Entry
Database: PDB / ID: 6yt0
TitleMagnesium chelatase H subunit (ChlH) E660D variant from Synechocystis sp.PCC6803
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
Biological speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 23, 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
B: Mg-chelatase subunit ChlH
A: Mg-chelatase subunit ChlH


Theoretical massNumber of molelcules
Total (without water)301,7152
Polymers301,7152
Non-polymers00
Water57632
1
B: Mg-chelatase subunit ChlH


Theoretical massNumber of molelcules
Total (without water)150,8571
Polymers150,8571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mg-chelatase subunit ChlH


Theoretical massNumber of molelcules
Total (without water)150,8571
Polymers150,8571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)321.787, 321.787, 104.919
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: 150857.469 Da / Num. of mol.: 2 / Mutation: E660D
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag and linker.
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Gene: chlH / Production host: Escherichia coli (E. coli) / References: UniProt: P73020
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.8-1.2 M sodium citrate and 2 mM dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.85→54.6 Å / Num. obs: 94580 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rpim(I) all: 0.061 / Net I/σ(I): 9.4
Reflection shellResolution: 2.85→2.9 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4748 / CC1/2: 0.56 / Rpim(I) all: 0.544 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Direct refinement from 6YSG

6ysg


Resolution: 2.85→54.6 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 15.983 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.767 / ESU R Free: 0.351
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2603 4709 5 %RANDOM
Rwork0.2091 ---
obs0.2116 89591 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 169.33 Å2 / Biso mean: 59.712 Å2 / Biso min: 13.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.35 Å20 Å2
2--0.69 Å20 Å2
3----2.25 Å2
Refinement stepCycle: final / Resolution: 2.85→54.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19327 0 0 32 19359
Biso mean---30.74 -
Num. residues----2455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01319717
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718223
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.63926742
X-RAY DIFFRACTIONr_angle_other_deg1.2491.57242337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.38552436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10223.1561071
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.442153373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.69615122
X-RAY DIFFRACTIONr_chiral_restr0.0770.22539
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222096
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023974
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 346 -
Rwork0.37 6602 -
all-6948 -
obs--99.19 %

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