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- PDB-6wh5: Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransf... -

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Basic information

Entry
Database: PDB / ID: 6wh5
TitleMycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to cob(II)alamin 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 / COBALAMIN / : / Corrinoid adenosyltransferase / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.866 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 7, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.classification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Corrinoid adenosyltransferase
B: Corrinoid adenosyltransferase
C: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95715
Polymers63,0023
Non-polymers4,95512
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-127 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.428, 62.678, 103.071
Angle α, β, γ (deg.)90.000, 119.040, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 20 or resid 22...
21(chain B and (resid 3 through 20 or resid 22...
31(chain C and (resid 3 through 20 or resid 22...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEU(chain A and (resid 3 through 20 or resid 22...AA3 - 206 - 23
12ASPASPASPASP(chain A and (resid 3 through 20 or resid 22...AA2225
13SERSERSERSER(chain A and (resid 3 through 20 or resid 22...AA2427
14GLUGLUGLUGLU(chain A and (resid 3 through 20 or resid 22...AA8386
15VALVALGLYGLY(chain A and (resid 3 through 20 or resid 22...AA3 - 1886 - 191
16VALVALGLYGLY(chain A and (resid 3 through 20 or resid 22...AA3 - 1886 - 191
17VALVALGLYGLY(chain A and (resid 3 through 20 or resid 22...AA3 - 1886 - 191
18VALVALGLYGLY(chain A and (resid 3 through 20 or resid 22...AA3 - 1886 - 191
21VALVALLEULEU(chain B and (resid 3 through 20 or resid 22...BB3 - 206 - 23
22ASPASPASPASP(chain B and (resid 3 through 20 or resid 22...BB2225
23SERSERSERSER(chain B and (resid 3 through 20 or resid 22...BB2427
24GLUGLUGLUGLU(chain B and (resid 3 through 20 or resid 22...BB8386
25VALVALGLYGLY(chain B and (resid 3 through 20 or resid 22...BB3 - 1886 - 191
26VALVALGLYGLY(chain B and (resid 3 through 20 or resid 22...BB3 - 1886 - 191
27VALVALGLYGLY(chain B and (resid 3 through 20 or resid 22...BB3 - 1886 - 191
28VALVALGLYGLY(chain B and (resid 3 through 20 or resid 22...BB3 - 1886 - 191
31VALVALLEULEU(chain C and (resid 3 through 20 or resid 22...CC3 - 206 - 23
32ASPASPASPASP(chain C and (resid 3 through 20 or resid 22...CC2225
33SERSERSERSER(chain C and (resid 3 through 20 or resid 22...CC2427
34LYSLYSHISHIS(chain C and (resid 3 through 20 or resid 22...CC86 - 8789 - 90
35VALVALGLYGLY(chain C and (resid 3 through 20 or resid 22...CC3 - 1886 - 191
36VALVALGLYGLY(chain C and (resid 3 through 20 or resid 22...CC3 - 1886 - 191
37VALVALGLYGLY(chain C and (resid 3 through 20 or resid 22...CC3 - 1886 - 191
38VALVALGLYGLY(chain C and (resid 3 through 20 or resid 22...CC3 - 1886 - 191

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Corrinoid adenosyltransferase


Mass: 21000.648 Da / Num. of mol.: 3
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, 218 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 3350, 0.1 M bis Tris 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: 1.127 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.866→54.156 Å / Num. obs: 46346 / % possible obs: 91.9 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Net I/σ(I): 12.2
Reflection shellResolution: 1.866→1.898 Å / Rmerge(I) obs: 0.745 / Num. unique obs: 12179 / CC1/2: 0.818

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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: 1.866→39.806 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.17
RfactorNum. reflection% reflection
Rfree0.2167 2372 5.12 %
Rwork0.1764 --
obs0.1784 46298 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.06 Å2 / Biso mean: 32.4085 Å2 / Biso min: 13.32 Å2
Refinement stepCycle: final / Resolution: 1.866→39.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 585 206 4995
Biso mean--41.68 32.56 -
Num. residues----558
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1653X-RAY DIFFRACTION0.601TORSIONAL
12B1653X-RAY DIFFRACTION0.601TORSIONAL
13C1653X-RAY DIFFRACTION0.601TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8663-1.90440.32981400.2686255691
1.9044-1.94580.24281350.2259276798
1.9458-1.99110.24611550.1924273699
1.9911-2.04090.21861660.195276699
2.0409-2.0960.3551630.284197235
2.096-2.15770.20071460.1809275699
2.1577-2.22730.20411450.1733273898
2.2273-2.30690.2081810.1997149853
2.3069-2.39930.19371570.1695276799
2.3993-2.50850.22411460.1686277798
2.5085-2.64070.22961360.1681270297
2.6407-2.80610.21071260.1826278699
2.8061-3.02270.21651590.17822822100
3.0227-3.32680.19131610.17542800100
3.3268-3.80780.23851610.17092791100
3.8078-4.79620.17671620.1484280398
4.7962-39.8060.24971330.1808288999
Refinement TLS params.Method: refined / Origin x: 11.119 Å / Origin y: -14.9474 Å / Origin z: 22.6985 Å
111213212223313233
T0.1545 Å20.001 Å2-0.0033 Å2-0.1486 Å2-0.0031 Å2--0.1427 Å2
L0.924 °20.0057 °20.1831 °2-1.1293 °20.0337 °2--1.1919 °2
S0.0048 Å °0.033 Å °0.0068 Å °-0.0498 Å °-0.0028 Å °-0.0522 Å °0.0069 Å °0.033 Å °-0.0019 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 188
2X-RAY DIFFRACTION1allB3 - 188
3X-RAY DIFFRACTION1allC3 - 188
4X-RAY DIFFRACTION1allD2 - 212
5X-RAY DIFFRACTION1allE1 - 3
6X-RAY DIFFRACTION1allF1 - 3
7X-RAY DIFFRACTION1allG301 - 303
8X-RAY DIFFRACTION1allH401 - 403

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