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

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Basic information

Entry
Database: PDB / ID: 6wgs
TitleMycobacterium tuberculosis pduO-type ATP:cobalamin adenosyltransferase bound to adenosylcobalamin
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
5'-DEOXYADENOSINE / COBALAMIN / Corrinoid adenosyltransferase / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 2.0Aug 4, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_source / entity / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_shell / struct_site_gen
Item: _diffrn_source.pdbx_wavelength_list / _entity.pdbx_number_of_molecules ..._diffrn_source.pdbx_wavelength_list / _entity.pdbx_number_of_molecules / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_site_gen.auth_seq_id
Description: Model orientation/position / Details: refined B12-Ado bond distance / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 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)22,5823
Polymers21,0011
Non-polymers1,5822
Water2,378132
1
A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules

A: Corrinoid adenosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7479
Polymers63,0023
Non-polymers4,7456
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 area13820 Å2
ΔGint-36 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.157, 87.157, 46.819
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-424-

HOH

21A-431-

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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 400 mM sodium phosphate monobasic/1600 mM potassium phosphate dibasic, 100 mM imidazole/HCl pH 8, and 200 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.5→46.82 Å / Num. obs: 33103 / % possible obs: 100 % / Redundancy: 9.9 % / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 1.292 / Num. unique obs: 1609 / CC1/2: 0.764

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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: 1.5→43.579 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1721 1628 4.92 %
Rwork0.1549 31450 -
obs0.1557 33078 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.85 Å2 / Biso mean: 29.7401 Å2 / Biso min: 12.57 Å2
Refinement stepCycle: final / Resolution: 1.5→43.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 198 132 1641
Biso mean--24.6 39.04 -
Num. residues----177
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.5-1.54420.23211300.20752592
1.5442-1.5940.22851310.18642576
1.594-1.6510.21391480.16932581
1.651-1.71710.16651310.15762610
1.7171-1.79530.15181310.15272610
1.7953-1.88990.18461420.15452580
1.8899-2.00830.18821510.15052587
2.0083-2.16340.15221180.15052641
2.1634-2.38110.14811360.13762606
2.3811-2.72560.17211190.14582667
2.7256-3.43370.16481460.15222649
3.4337-43.5790.17611450.16122751
Refinement TLS params.Method: refined / Origin x: -30.2742 Å / Origin y: 25.0437 Å / Origin z: 16.088 Å
111213212223313233
T0.1022 Å2-0.0109 Å20.0079 Å2-0.1676 Å2-0.015 Å2--0.1551 Å2
L1.1578 °2-0.0323 °20.0256 °2-2.3171 °2-0.295 °2--1.2652 °2
S0.0104 Å °0.0393 Å °-0.0178 Å °-0.0304 Å °0.0056 Å °-0.2684 Å °-0.0063 Å °0.1693 Å °0.0014 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA11 - 188
2X-RAY DIFFRACTION1allA201 - 301
3X-RAY DIFFRACTION1allS1 - 172

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