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- PDB-9vio: Crystal strcture of adenosylcobinamide kinase/adenosylcobinamide ... -

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Basic information

Entry
Database: PDB / ID: 9vio
TitleCrystal strcture of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU from Akkermansia muciniphila, crystal form I
ComponentsAdenosylcobinamide kinase
KeywordsTRANSFERASE / VB12 / Cobamide remodeling / CobU / adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase / Akkermansia muciniphila
Function / homology
Function and homology information


adenosylcobinamide kinase activity / adenosylcobinamide kinase / adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / GTP binding / ATP binding
Similarity search - Function
Cobinamide kinase/cobinamide phosphate guanyltransferase / Cobinamide kinase / cobinamide phosphate guanyltransferase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MALONIC ACID / Adenosylcobinamide kinase
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJiang, M. / Kong, C. / Wei, Q. / Guo, S. / Chen, X. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2108085MC75 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Structural insights into the adenosylcobinamide-phosphate guanylyltransferase activity of CobU from Akkermansia muciniphila.
Authors: Jiang, M. / Kong, C. / Wei, Q. / Guo, S. / Chen, X. / Li, Q. / Wang, M.
History
DepositionJun 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosylcobinamide kinase
B: Adenosylcobinamide kinase
C: Adenosylcobinamide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6346
Polymers66,3223
Non-polymers3123
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-67 kcal/mol
Surface area21500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.186, 55.184, 98.408
Angle α, β, γ (deg.)90.00, 100.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenosylcobinamide kinase / Adenosylcobinamide-phosphate guanylyltransferase


Mass: 22107.193 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila ATCC BAA-835 (bacteria)
Gene: Amuc_1678 / Production host: Escherichia coli (E. coli)
References: UniProt: B2UM52, adenosylcobinamide kinase, adenosylcobinamide-phosphate guanylyltransferase
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.14 Å3/Da / Density % sol: 42.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% Tacsimate pH 8.0, 16% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38184 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Χ2: 0.936 / Net I/σ(I): 6.6 / Num. measured all: 256080
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.076.41.09838040.7230.9160.4711.1970.93100
2.07-2.156.70.76637630.8520.9590.3170.8310.919100
2.15-2.256.80.56338080.9170.9780.2310.6090.937100
2.25-2.376.80.36437840.9650.9910.150.3940.935100
2.37-2.526.70.22238320.9820.9950.0920.2410.948100
2.52-2.716.80.15137760.9910.9980.0630.1640.952100
2.71-2.996.70.09338270.9950.9990.0380.1010.975100
2.99-3.426.80.05938290.9970.9990.0250.0640.978100
3.42-4.316.80.04438420.99810.0180.0480.97699.9
4.31-506.60.03339190.99910.0140.0360.80799.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28.1 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 1981 5.19 %
Rwork0.1977 --
obs0.1996 38133 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 21 355 4248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053974
X-RAY DIFFRACTIONf_angle_d0.8235384
X-RAY DIFFRACTIONf_dihedral_angle_d13.0981474
X-RAY DIFFRACTIONf_chiral_restr0.052625
X-RAY DIFFRACTIONf_plane_restr0.006689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.35571400.31432601X-RAY DIFFRACTION100
2.05-2.110.30351420.28722521X-RAY DIFFRACTION100
2.11-2.170.28711330.26592567X-RAY DIFFRACTION100
2.17-2.240.30881230.25092589X-RAY DIFFRACTION100
2.24-2.320.27711660.23692584X-RAY DIFFRACTION100
2.32-2.410.25611590.22142527X-RAY DIFFRACTION100
2.41-2.520.30951300.22232590X-RAY DIFFRACTION100
2.52-2.650.24941390.21912576X-RAY DIFFRACTION100
2.65-2.820.24941450.2122548X-RAY DIFFRACTION100
2.82-3.040.23111320.20592597X-RAY DIFFRACTION100
3.04-3.340.23391500.19252604X-RAY DIFFRACTION100
3.34-3.820.21941390.16722583X-RAY DIFFRACTION100
3.82-4.810.17651470.14872599X-RAY DIFFRACTION100
4.81-28.10.18241360.16112666X-RAY DIFFRACTION99

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