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- PDB-6ytn: Magnesium chelatase H subunit (ChlH) E660W variant from Synechocy... -

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Basic information

Entry
Database: PDB / ID: 6ytn
TitleMagnesium chelatase H subunit (ChlH) E660W variant from Synechocystis sp.PCC6803
ComponentsMg-chelatase subunit ChlH
KeywordsPHOTOSYNTHESIS / Magnesium chelatase / chlorophyll
Function / homologyMagnesium-chelatase, subunit H / Magnesium chelatase, subunit H, N-terminal / Domain of unknown function (DUF3479) / magnesium chelatase / magnesium chelatase activity / CobN/magnesium chelatase / CobN/Magnesium Chelatase / chlorophyll biosynthetic process / magnesium chelatase
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 24, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Mg-chelatase subunit ChlH
BBB: Mg-chelatase subunit ChlH


Theoretical massNumber of molelcules
Total (without water)301,8572
Polymers301,8572
Non-polymers00
Water1448
1
AAA: Mg-chelatase subunit ChlH


Theoretical massNumber of molelcules
Total (without water)150,9291
Polymers150,9291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Mg-chelatase subunit ChlH


Theoretical massNumber of molelcules
Total (without water)150,9291
Polymers150,9291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)317.550, 317.550, 104.430
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: 150928.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag and linker / Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: chlH / Production host: Escherichia coli (E. coli) / References: UniProt: P73020
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→79.39 Å / Num. obs: 107741 / % possible obs: 99.9 % / Redundancy: 5.8 % / CC1/2: 0.997 / Rpim(I) all: 0.059 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.77 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7995 / CC1/2: 0.49 / Rpim(I) all: 0.676

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YSG

6ysg


Resolution: 2.7→79.387 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.547 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.283
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2346 5365 4.98 %
Rwork0.1919 --
all0.194 --
obs-107741 99.904 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.301 Å2
Baniso -1Baniso -2Baniso -3
1-1.288 Å20.644 Å20 Å2
2--1.288 Å20 Å2
3----4.179 Å2
Refinement stepCycle: LAST / Resolution: 2.7→79.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19763 0 0 8 19771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01320156
X-RAY DIFFRACTIONr_bond_other_d0.0010.01718666
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.63827330
X-RAY DIFFRACTIONr_angle_other_deg1.1431.57143364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73452489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83423.1341088
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.431153467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.80415124
X-RAY DIFFRACTIONr_chiral_restr0.0520.22594
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222564
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024064
X-RAY DIFFRACTIONr_nbd_refined0.1930.24150
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.217726
X-RAY DIFFRACTIONr_nbtor_refined0.1550.29568
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.29005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2386
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1170.231
X-RAY DIFFRACTIONr_nbd_other0.1640.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.28
X-RAY DIFFRACTIONr_mcbond_it3.8447.32410016
X-RAY DIFFRACTIONr_mcbond_other3.8397.32410015
X-RAY DIFFRACTIONr_mcangle_it5.94710.97612485
X-RAY DIFFRACTIONr_mcangle_other5.94710.97612486
X-RAY DIFFRACTIONr_scbond_it3.5837.6310140
X-RAY DIFFRACTIONr_scbond_other3.5837.63110141
X-RAY DIFFRACTIONr_scangle_it5.70311.30514845
X-RAY DIFFRACTIONr_scangle_other5.70311.30514846
X-RAY DIFFRACTIONr_lrange_it8.26284.7521860
X-RAY DIFFRACTIONr_lrange_other8.26184.75421860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.7-2.770.3584320.33375560.33579900.6950.71499.9750.333
2.77-2.8460.3593950.31773660.31977610.7590.7831000.317
2.846-2.9280.3273650.28372060.28575720.820.84199.98680.283
2.928-3.0180.3383490.26869990.27173480.8290.8511000.268
3.018-3.1170.3193220.25167880.25471100.8380.8781000.251
3.117-3.2260.2883540.23565080.23868630.8760.89999.98540.235
3.226-3.3480.283370.21863040.22166430.8830.91499.96990.218
3.348-3.4840.2673110.20560920.20864030.9020.9251000.205
3.484-3.6390.2442930.19758090.19961060.9220.93399.93450.197
3.639-3.8160.2162750.18255610.18458410.9290.94699.91440.182
3.816-4.0220.2193120.17552920.17856090.9380.94799.91090.175
4.022-4.2650.222770.16249700.16552570.9430.95399.80980.162
4.265-4.5590.2052580.14946990.15249650.9440.95899.83890.149
4.559-4.9230.1932150.14343660.14545900.9560.96699.80390.143
4.923-5.3910.21880.1640220.16242230.950.95999.69220.16
5.391-6.0240.2271490.19137000.19338530.9290.93799.89620.191
6.024-6.9490.2121870.16832130.17134030.9440.95299.91180.168
6.949-8.4940.171640.14226760.14428470.9620.96699.75410.142
8.494-11.9440.1491160.1420880.1422180.9760.97599.36880.14
11.944-79.3870.287660.26211640.26412410.9030.9299.11360.262

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