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- PDB-3gaj: Structure of a C-terminal deletion variant of a PduO-type ATP:cor... -

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Basic information

Entry
Database: PDB / ID: 3gaj
TitleStructure of a C-terminal deletion variant of a 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 / 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 / COBALAMIN / : / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.38 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: 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 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,4345
Polymers21,5331
Non-polymers1,9014
Water3,009167
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)70,30315
Polymers64,6003
Non-polymers5,70312
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 area17280 Å2
ΔGint-98 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.679, 67.679, 111.180
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-282-

HOH

DetailsThe trimer is generated by the following symmetry operations: [-y, x-y, z + (0 1 0)] and [-x+y, -x, z + (-1 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: 21533.369 Da / Num. of mol.: 1 / Mutation: C-terminal truncation at residue 183
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 , 5 types, 171 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-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


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


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
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: 1.38→50 Å / Num. obs: 38038 / % possible obs: 97.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.063 / Χ2: 2.527 / Net I/σ(I): 47.679
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.38-1.433.10.09731921.303182
1.43-1.493.80.0935861.607191.7
1.49-1.555.10.08438771.773199.9
1.55-1.645.40.07439461.7651100
1.64-1.745.40.06739311.9551100
1.74-1.875.40.0638652.1411100
1.87-2.065.40.05539342.6571100
2.06-2.3610.60.07838852.6031100
2.36-2.9710.40.07139242.991100
2.97-507.90.05238983.912199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.38→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.713 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 1902 5 %RANDOM
Rwork0.164 ---
obs0.165 38032 97.34 %-
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 max: 46.39 Å2 / Biso mean: 14.355 Å2 / Biso min: 5.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 99 167 1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221646
X-RAY DIFFRACTIONr_angle_refined_deg1.9552.0232274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1755190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.424.69983
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10915256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9251510
X-RAY DIFFRACTIONr_chiral_restr0.2110.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021286
X-RAY DIFFRACTIONr_nbd_refined0.2210.2772
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2119
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3530.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0560.22
X-RAY DIFFRACTIONr_mcbond_it0.7031.5933
X-RAY DIFFRACTIONr_mcangle_it1.30721514
X-RAY DIFFRACTIONr_scbond_it2.0163724
X-RAY DIFFRACTIONr_scangle_it3.114.5760
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.167 107 -
Rwork0.159 2222 -
all-2329 -
obs--80.31 %

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