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- PDB-3ci4: Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase f... -

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Basic information

Entry
Database: PDB / ID: 3ci4
TitleStructure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)inamide and ATP
ComponentsCobalamin adenosyltransferase PduO-like protein
KeywordsTRANSFERASE / adenosyltransferase variant / ATP binding / corrin 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 / COB(II)INAMIDE / : / Corrinoid adenosyltransferase
Similarity search - Component
Biological speciesLactobacillus reuteri (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)23,9435
Polymers22,3821
Non-polymers1,5614
Water1,53185
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)71,82915
Polymers67,1473
Non-polymers4,68212
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 area14880 Å2
ΔGint-59.7 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.826, 67.826, 111.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1059-

HOH

21A-1061-

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, 89 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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-CBY / COB(II)INAMIDE


Mass: 990.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H72CoN11O8
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 44.1 %
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 dicyanocobinamide, 2 mM MgCl2, 2 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: 2→30 Å / Num. obs: 13603 / % possible obs: 98.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.7
Reflection shellHighest resolution: 2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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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: 2→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU B: 3.579 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20927 622 4.9 %RANDOM
Rwork0.16996 ---
obs0.17188 12024 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.122 Å2
Baniso -1Baniso -3Baniso -2
1-0.21 Å20 Å2-
2--0 Å20.21 Å2
3---0.32 Å2-
Refine analyzeLuzzati coordinate error obs: 0.191 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 101 85 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9932.0252225
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0195186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65724.60576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04315244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.22159
X-RAY DIFFRACTIONr_chiral_restr0.1970.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021237
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2766
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21130
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.284
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0940.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.571.5933
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99321501
X-RAY DIFFRACTIONr_scbond_it1.7243692
X-RAY DIFFRACTIONr_scangle_it2.5234.5724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 43 -
Rwork0.196 756 -
obs--87.23 %

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