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- PDB-6wgv: Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransf... -

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Basic information

Entry
Database: PDB / ID: 6wgv
TitleMycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to adenosylcobalamin and PPPi
ComponentsCorrinoid adenosyltransferase
KeywordsTRANSFERASE / chaperone / B12 trafficking
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / porphyrin-containing compound biosynthetic process / cobalamin biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily
Similarity search - Domain/homology
TRIPHOSPHATE / 5'-DEOXYADENOSINE / COBALAMIN / Corrinoid adenosyltransferase / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsMascarenhas, R.N. / Ruetz, M. / Koutmos, M. / Banerjee, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1-DK45776 United States
American Heart Association19POST34370113 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Mobile loop dynamics in adenosyltransferase control binding and reactivity of coenzyme B 12 .
Authors: Mascarenhas, R. / Ruetz, M. / McDevitt, L. / Koutmos, M. / Banerjee, R.
History
DepositionApr 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8655
Polymers21,0011
Non-polymers1,8644
Water27015
1
A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,59415
Polymers63,0023
Non-polymers5,59212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area14820 Å2
ΔGint-82 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.631, 87.631, 46.554
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Corrinoid adenosyltransferase


Mass: 21000.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: E5M05_13560, ERS023446_03354, ERS027651_01619, FCN16_21305, SAMEA2682864_01680, SAMEA2683035_01578
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045JVI3, UniProt: P9WP99*PLUS, corrinoid adenosyltransferase

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Non-polymers , 5 types, 19 molecules

#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 26% PEG 3350, 0.1M bisTris pH 6.5, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.15→39.683 Å / Num. obs: 11342 / % possible obs: 99.1 % / Redundancy: 6.3 % / CC1/2: 0.972 / Rmerge(I) obs: 0.176 / Net I/σ(I): 6.6
Reflection shellResolution: 2.15→2.22 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 906 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G2D

2g2d


Resolution: 2.151→39.683 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 552 4.87 %
Rwork0.1883 10786 -
obs0.1898 11338 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.42 Å2 / Biso mean: 44.5426 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: final / Resolution: 2.151→39.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 225 15 1540
Biso mean--40.71 33.63 -
Num. residues----173
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.151-2.36710.27171550.2202260297
2.3671-2.70960.25081270.20012691100
2.7096-3.41350.23741460.2034268099
3.4135-39.6830.18781240.171281399

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