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- PDB-3gai: Structure of a F112A variant PduO-type ATP:corrinoid adenosyltran... -

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Basic information

Entry
Database: PDB / ID: 3gai
TitleStructure of a F112A variant PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP
ComponentsCobalamin adenosyltransferase PduO-like protein
KeywordsTRANSFERASE
Function / homology
Function and homology information


corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / cobalamin biosynthetic process / ATP 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 / COBALAMIN / : / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å
AuthorsSt Maurice, M. / Mera, P.E. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: Biochemistry / Year: 2009
Title: Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the ...Title: Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme.
Authors: Mera, P.E. / St Maurice, M. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionFeb 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,59311
Polymers22,3061
Non-polymers2,28710
Water2,864159
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)73,78033
Polymers66,9193
Non-polymers6,86230
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 area16020 Å2
ΔGint-111 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.745, 80.745, 89.693
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

DetailsThe trimer is generated by the following symmetry operations: [-y, x-y, z + (0 0 0)] and [-x+y, -x, z + (0 0 0)]

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cobalamin adenosyltransferase PduO-like protein


Mass: 22306.221 Da / Num. of mol.: 1 / Mutation: F112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: CRL1098 / Gene: cobA, pduo / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50EJ2, corrinoid adenosyltransferase

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Non-polymers , 7 types, 169 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: anoxic, 14% PEG 8000, 0.2M potassium chloride, 0.1 M MES, 30 ug/mL E. coli FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydoxycobalamin, 10 mM ATP, 10 mM magnesium chloride, 0.3 M sodium ...Details: anoxic, 14% PEG 8000, 0.2M potassium chloride, 0.1 M MES, 30 ug/mL E. coli FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydoxycobalamin, 10 mM ATP, 10 mM magnesium chloride, 0.3 M sodium chloride , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorType: SBC-3 / Detector: CCD / Date: Aug 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 36190 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.057 / Χ2: 2.826 / Net I/σ(I): 46.235
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.48-1.5350.12836181.121198.6
1.53-1.595.40.11635871.2451100
1.59-1.675.40.136441.5091100
1.67-1.755.50.08936341.8671100
1.75-1.865.50.08236082.3391100
1.86-2.015.40.06936482.8481100
2.01-2.215.40.06536313.9061100
2.21-2.535.40.05936244.4361100
2.53-3.1960.06635734.945198.9
3.19-506.50.04936233.497199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.48→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.867 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1804 5 %RANDOM
Rwork0.156 ---
obs0.157 36185 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.11 Å2 / Biso mean: 19.396 Å2 / Biso min: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.48→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1463 0 145 159 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221738
X-RAY DIFFRACTIONr_angle_refined_deg2.2012.0512413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9555208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17724.77388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80215284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2721512
X-RAY DIFFRACTIONr_chiral_restr0.2710.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021337
X-RAY DIFFRACTIONr_nbd_refined0.2360.2820
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21212
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2104
X-RAY DIFFRACTIONr_metal_ion_refined0.1340.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.2117
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.246
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1780.21
X-RAY DIFFRACTIONr_mcbond_it0.8281.5949
X-RAY DIFFRACTIONr_mcangle_it1.47121555
X-RAY DIFFRACTIONr_scbond_it2.3423805
X-RAY DIFFRACTIONr_scangle_it3.4774.5843
LS refinement shellResolution: 1.481→1.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 136 -
Rwork0.15 2498 -
all-2634 -
obs--97.74 %

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