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- PDB-6wgu: Mycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase -

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Basic information

Entry
Database: PDB / ID: 6wgu
TitleMycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase
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
Corrinoid adenosyltransferase / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)21,3855
Polymers21,0011
Non-polymers3844
Water1,47782
1
A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,15515
Polymers63,0023
Non-polymers1,15312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6830 Å2
ΔGint-166 kcal/mol
Surface area20670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.418, 130.418, 130.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-382-

HOH

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Components

#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
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.75 % PEG 400, 1.5 M ammonium sulfate, 100 mM sodium acetate/acetic acid pH 5.5

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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 EIGER 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: 1.65→34.86 Å / Num. obs: 22879 / % possible obs: 99.3 % / Redundancy: 31.9 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 31.9
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 1.103 / Num. unique obs: 1013 / CC1/2: 0.73

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
Aimlessdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G2D

2g2d


Resolution: 1.65→30.74 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.09
RfactorNum. reflection% reflection
Rfree0.1785 1208 5.29 %
Rwork0.1606 --
obs0.1615 22845 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.3 Å2 / Biso mean: 37.6302 Å2 / Biso min: 16.49 Å2
Refinement stepCycle: final / Resolution: 1.65→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 20 82 1294
Biso mean--91.6 41.66 -
Num. residues----159
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6505-1.71650.24171150.2286223994
1.7165-1.79470.21231220.19322379100
1.7947-1.88930.171400.16632373100
1.8893-2.00760.16411290.15942388100
2.0076-2.16260.16831310.14952394100
2.1626-2.38010.15211430.13832392100
2.3801-2.72440.1911520.14742425100
2.7244-3.43170.20611450.15912452100
3.4317-30.740.16491310.16492595100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.9115.72074.23389.40513.80275.2037-0.0274-0.11440.3550.2061-0.15590.2982-0.2827-0.12530.21910.25080.01660.02670.19780.05180.225859.37468.58172.809
25.75334.9123.32898.06085.18756.1269-0.0399-0.062-0.02310.0832-0.0180.1687-0.2102-0.41910.06820.20770.02210.06040.23610.05440.231952.0563.21977.609
32.0815-1.91031.93334.5279-2.91892.26790.13782.6944-1.1638-0.0006-0.7094-1.29160.61662.17361.04960.48640.06860.04860.8695-0.06360.694749.07680.30893.881
41.9772-1.2042-1.54034.32015.01296.7201-0.0638-0.118-0.03160.4738-0.04850.06580.0332-0.24570.1250.2006-0.00890.07460.23090.05740.207654.35157.38785.607
52.8153.6857-2.67626.0224-2.56183.3021-0.2444-0.3452-0.84570.5486-0.2691-0.39290.45270.49880.32080.34370.08380.06890.25270.0940.381268.2444.88671.689
62.90662.461.79877.21835.36256.65560.0216-0.1414-0.04060.10190.0727-0.2589-0.00160.2578-0.17330.16670.01910.02540.2030.04140.17765.5862.51775.594
71.3378-1.0991-0.83928.19696.72698.1528-0.0364-0.2748-0.04080.19730.2092-0.4668-0.01930.1826-0.16710.18960.01370.04230.21160.0560.198562.18160.3882.356
82.27820.1470.66766.0781-0.42557.0239-0.47890.4817-1.8721-0.07960.0551-0.16460.8990.31030.26240.42620.05210.14790.21870.00420.394169.98843.37667.208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 29:53 )A29 - 53
2X-RAY DIFFRACTION2( CHAIN A AND RESID 54:82 )A54 - 82
3X-RAY DIFFRACTION3( CHAIN A AND RESID 83:87 )A83 - 87
4X-RAY DIFFRACTION4( CHAIN A AND RESID 88:110 )A88 - 110
5X-RAY DIFFRACTION5( CHAIN A AND RESID 111:123 )A111 - 123
6X-RAY DIFFRACTION6( CHAIN A AND RESID 124:149 )A124 - 149
7X-RAY DIFFRACTION7( CHAIN A AND RESID 150:175 )A150 - 175
8X-RAY DIFFRACTION8( CHAIN A AND RESID 176:187 )A176 - 187

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