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- PDB-6ys9: T_926 truncate of ChlH from Thermosynechococcus elongatus at 1.64... -

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Basic information

Entry
Database: PDB / ID: 6ys9
TitleT_926 truncate of ChlH from Thermosynechococcus elongatus at 1.64 A resolution
ComponentsMagnesium-protoporphyrin methyltransferase
KeywordsPHOTOSYNTHESIS / Magnesium chelatase / chlorophyll / bacteriochlorophyll
Function / homology
Function and homology information


magnesium chelatase / magnesium chelatase activity / chlorophyll biosynthetic process / photosynthesis / methyltransferase activity / methylation / 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
: / magnesium chelatase
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 21, 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 1.2May 1, 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: Magnesium-protoporphyrin methyltransferase
B: Magnesium-protoporphyrin methyltransferase
C: Magnesium-protoporphyrin methyltransferase
D: Magnesium-protoporphyrin methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,5318
Polymers184,3754
Non-polymers1564
Water9,980554
1
A: Magnesium-protoporphyrin methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1332
Polymers46,0941
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Magnesium-protoporphyrin methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1332
Polymers46,0941
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Magnesium-protoporphyrin methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1332
Polymers46,0941
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Magnesium-protoporphyrin methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1332
Polymers46,0941
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.480, 140.330, 78.010
Angle α, β, γ (deg.)90.000, 108.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Magnesium-protoporphyrin methyltransferase


Mass: 46093.746 Da / Num. of mol.: 4 / Mutation: Truncated at the N-terminus
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Gene: chlH / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DM52
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20-22% PEG 6000, 100 mM Tris pH 8, 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97633 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.893
11-L, -K, -H20.107
ReflectionResolution: 1.64→64.38 Å / Num. obs: 172739 / % possible obs: 91.2 % / Redundancy: 2.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.057 / Rrim(I) all: 0.093 / Net I/σ(I): 7.4
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.544 / Num. unique obs: 10643 / CC1/2: 0.487 / Rpim(I) all: 0.442 / Rrim(I) all: 0.704 / % possible all: 76.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.5.1data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet poly-Ala model

Resolution: 1.64→64.38 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 1.91 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 8572 5 %RANDOM
Rwork0.2008 ---
obs0.203 164121 86.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 200 Å2 / Biso mean: 24.569 Å2 / Biso min: 2.32 Å2
Baniso -1Baniso -2Baniso -3
1--3.54 Å20 Å2-0.25 Å2
2--2.95 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 1.64→64.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12018 0 4 554 12576
Biso mean--28.01 23.65 -
Num. residues----1519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01312234
X-RAY DIFFRACTIONr_bond_other_d0.0090.01711320
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.63816596
X-RAY DIFFRACTIONr_angle_other_deg1.4191.57326202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41751511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02922.514700
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.266152123
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7841596
X-RAY DIFFRACTIONr_chiral_restr0.0770.21603
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213755
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022573
LS refinement shellResolution: 1.611→1.653 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 158 -
Rwork0.246 3225 -
all-3383 -
obs--22.84 %

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