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

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Basic information

Entry
Database: PDB / ID: 9vip
TitleCrystal strcture of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase CobU from Akkermansia muciniphila, crystal form II
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
Adenosylcobinamide kinase
Similarity search - Component
Biological speciesAkkermansia muciniphila ATCC BAA-835 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1992
Polymers22,1071
Non-polymers921
Water45025
1
A: Adenosylcobinamide kinase
hetero molecules

A: Adenosylcobinamide kinase
hetero molecules

A: Adenosylcobinamide kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5986
Polymers66,3223
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area5880 Å2
ΔGint-46 kcal/mol
Surface area24350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.115, 88.115, 88.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

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Components

#1: Protein Adenosylcobinamide kinase / Adenosylcobinamide-phosphate guanylyltransferase


Mass: 22107.193 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05M cesium chloride, 0.1M MES monohydrate pH 7.0, 26% Jeffamine M-600, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 10366 / % possible obs: 100 % / Redundancy: 36.5 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.019 / Rrim(I) all: 0.105 / Χ2: 0.964 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.3-2.3840.11.74410010.8860.9690.2781.7660.911
2.38-2.4839.41.1710070.9490.9870.1881.1850.938
2.48-2.5940.20.75110460.9660.9910.120.760.961
2.59-2.7338.60.53110130.9810.9950.0860.5381.012
2.73-2.938.60.33110310.9930.9980.0540.3351.007
2.9-3.1238.40.2210250.9960.9990.0360.2230.958
3.12-3.4435.50.1510380.9970.9990.0260.1520.996
3.44-3.9333.60.1110350.99810.020.1120.966
3.93-4.9531.30.08910560.99910.0170.0910.941
4.95-5030.50.07711140.99910.0150.0780.95

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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: 2.3→29.37 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 509 4.94 %
Rwork0.2031 --
obs0.2048 10306 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1347 0 6 25 1378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051379
X-RAY DIFFRACTIONf_angle_d0.711869
X-RAY DIFFRACTIONf_dihedral_angle_d13.509504
X-RAY DIFFRACTIONf_chiral_restr0.046216
X-RAY DIFFRACTIONf_plane_restr0.006239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.34211140.30052393X-RAY DIFFRACTION98
2.54-2.90.31021410.24182403X-RAY DIFFRACTION100
2.9-3.650.31561410.26942436X-RAY DIFFRACTION100
3.66-29.370.19071130.16942565X-RAY DIFFRACTION100

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