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- PDB-7c6o: Catalytic Subunit of Cobaltochelatase from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7c6o
TitleCatalytic Subunit of Cobaltochelatase from Mycobacterium tuberculosis
ComponentsCobalamin biosynthesis protein CobN
KeywordsLIGASE / Co-CHELATASE / METAL BINDING PROTEIN
Function / homology
Function and homology information


cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / plasma membrane / cytosol
Similarity search - Function
Cobaltochelatase, CobN subunit / CobN/magnesium chelatase / CobN/Magnesium Chelatase
Similarity search - Domain/homology
Cobalamin biosynthesis protein CobN / Cobalamin biosynthesis protein CobN
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsZhang, J. / Liu, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870729 China
Ministry of Science and Technology (MoST, China)2017YFA0503703 China
CitationJournal: Proteins / Year: 2021
Title: Crystal structure of the large subunit of cobaltochelatase from Mycobacterium tuberculosis.
Authors: Zhang, J.H. / Yuan, H. / Wang, X. / Dai, H.E. / Zhang, M. / Liu, L.
History
DepositionMay 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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: Cobalamin biosynthesis protein CobN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5736
Polymers133,1821
Non-polymers3915
Water17,294960
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area40550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.564, 125.473, 78.551
Angle α, β, γ (deg.)90.000, 103.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cobalamin biosynthesis protein CobN / Cobaltochelatase subunit CobN


Mass: 133181.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: cobN, DSI38_03330, ERS023446_03562, ERS094182_01916, F6W99_00653, GJE03_10820
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0T5XW27, UniProt: O53498*PLUS, cobaltochelatase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 289 K / Method: liquid diffusion / Details: PEG 10,000, Ethylene glycol, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 110491 / % possible obs: 97.1 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Net I/σ(I): 21.2
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 10924 / CC1/2: 0.743 / Rpim(I) all: 0.47 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549: ???refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZHJ

4zhj


Resolution: 1.801→48.501 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 5171 5.09 %
Rwork0.1633 --
obs0.165 101590 89.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.33 Å2 / Biso mean: 24.3623 Å2 / Biso min: 8.43 Å2
Refinement stepCycle: final / Resolution: 1.801→48.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8903 0 25 960 9888
Biso mean--40.72 35.1 -
Num. residues----1173
Refinement TLS params.Method: refined / Origin x: -24.531 Å / Origin y: -4.954 Å / Origin z: -31.648 Å
111213212223313233
T0.0955 Å2-0.0007 Å20.0091 Å2-0.0938 Å2-0.0204 Å2--0.105 Å2
L0.2629 °2-0.2267 °20.2136 °2-0.283 °2-0.2398 °2--0.2871 °2
S0.0055 Å °-0.0066 Å °-0.0222 Å °0.0124 Å °-0.005 Å °0.0019 Å °0.0013 Å °-0.0283 Å °0.0026 Å °
Refinement TLS groupSelection details: all

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