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- PDB-2r6x: Structure of a D35N variant PduO-type ATP:co(I)rrinoid adenosyltr... -

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Basic information

Entry
Database: PDB / ID: 2r6x
TitleStructure of a D35N variant PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with ATP
ComponentsCobalamin adenosyltransferase PduO-like protein
KeywordsTRANSFERASE / adenosyltransferase variant / ATP binding
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / cobalamin biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.61 Å
AuthorsSt Maurice, M. / Mera, P.E. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and functional analyses of the human-type corrinoid adenosyltransferase (PduO) from Lactobacillus reuteri.
Authors: Mera, P.E. / St Maurice, M. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionSep 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cobalamin adenosyltransferase PduO-like protein
B: Cobalamin adenosyltransferase PduO-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8748
Polymers44,7632
Non-polymers1,1126
Water2,504139
1
A: Cobalamin adenosyltransferase PduO-like protein
hetero molecules

A: Cobalamin adenosyltransferase PduO-like protein
hetero molecules

A: Cobalamin adenosyltransferase PduO-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,81112
Polymers67,1443
Non-polymers1,6679
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12160 Å2
MethodPISA
2
B: Cobalamin adenosyltransferase PduO-like protein
hetero molecules

B: Cobalamin adenosyltransferase PduO-like protein
hetero molecules

B: Cobalamin adenosyltransferase PduO-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,81112
Polymers67,1443
Non-polymers1,6679
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.772, 64.772, 169.438
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-1023-

HOH

21A-1040-

HOH

31B-1057-

HOH

DetailsThe biological unit is a trimer. There are two monomers in the asymmetric unit. Each monomer forms its own biological unit. The biological units are generated from the operations: -x+y, -x, z and -y, x-y, z.

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Components

#1: Protein Cobalamin adenosyltransferase PduO-like protein


Mass: 22381.332 Da / Num. of mol.: 2 / Mutation: D35N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: CRL1098 / Gene: cobA / Plasmid: pET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q50EJ2, corrinoid adenosyltransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 6
Details: ANOXIC, 16% PEG 8000, 0.1 M MES, 200 mM KCl, 30 ug/mL FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydroxycobalamin, 10 mM MgCl2, 10 mM ATP, pH 6.0, vapor diffusion, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 25, 2007 / Details: Montel
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.61→30 Å / Num. obs: 12422 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 6.8 / Net I/σ(I): 26.1
Reflection shellResolution: 2.61→2.66 Å / Redundancy: 4.9 % / Rsym value: 0.177 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3data extraction
RefinementResolution: 2.61→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.862 / SU B: 10.706 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 579 4.9 %RANDOM
Rwork0.173 ---
obs0.177 11938 96.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.817 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.61→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 66 139 2986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222912
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9723977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57424.621145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.67915463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1781517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022221
X-RAY DIFFRACTIONr_nbd_refined0.2010.21402
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2129
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.2139
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.233
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0910.22
X-RAY DIFFRACTIONr_mcbond_it0.5931.51786
X-RAY DIFFRACTIONr_mcangle_it0.85922815
X-RAY DIFFRACTIONr_scbond_it1.49931284
X-RAY DIFFRACTIONr_scangle_it2.1144.51156
LS refinement shellResolution: 2.61→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 38 -
Rwork0.196 764 -
all-802 -
obs--92.08 %

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