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- PDB-3ci1: Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase f... -

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Basic information

Entry
Database: PDB / ID: 3ci1
TitleStructure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP
ComponentsCobalamin adenosyltransferase PduO-like protein
KeywordsTRANSFERASE / adenosyltransferase / ATP binding / four-coordinate cob(II)alamin
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 / Resolution: 1.9 Å
AuthorsMaurice, M.St. / Mera, P.E. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: Biochemistry / Year: 2008
Title: Structural characterization of a human-type corrinoid adenosyltransferase confirms that coenzyme B12 is synthesized through a four-coordinate intermediate.
Authors: St Maurice, M. / Mera, P. / Park, K. / Brunold, T.C. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Non-polymer description
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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

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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)24,2835
Polymers22,3821
Non-polymers1,9014
Water2,684149
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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)72,85015
Polymers67,1473
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 area15270 Å2
ΔGint-58.9 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.814, 67.814, 111.163
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-1047-

HOH

21A-1123-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cobalamin adenosyltransferase PduO-like protein


Mass: 22382.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: CRL1098 / Gene: cobA / 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, 153 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 6
Details: ANOXIC, 13% PEG 8000, 0.1 M MES, 200 mM KCl, 33 ug/mL FMN reductase, 20 mM NADH, 2 mM FMN, 2 mM hydroxycobalamin, 3 mM MgCl2, 3 mM ATP, pH 6, 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: 1.9→30 Å / Num. obs: 16892 / % possible obs: 97.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
MOLREPphasing
RefinementResolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.82 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 731 4.9 %RANDOM
Rwork0.155 ---
obs0.157 14785 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.175 Å
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1487 0 105 149 1741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221644
X-RAY DIFFRACTIONr_angle_refined_deg2.0452.0312268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6025190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85924.74478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28915255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.93159
X-RAY DIFFRACTIONr_chiral_restr0.2020.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021257
X-RAY DIFFRACTIONr_nbd_refined0.2180.2811
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21155
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2113
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.227
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0420.23
X-RAY DIFFRACTIONr_mcbond_it0.6671.5942
X-RAY DIFFRACTIONr_mcangle_it1.08721520
X-RAY DIFFRACTIONr_scbond_it1.933712
X-RAY DIFFRACTIONr_scangle_it2.7444.5746
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 49 -
Rwork0.175 1043 -
all-1092 -
obs--98.11 %

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