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- PDB-8ykc: Crystal structure of adenosylcobinamide kinase / adenosylcobinami... -

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Basic information

Entry
Database: PDB / ID: 8ykc
TitleCrystal structure of adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase complexed with GDP
ComponentsBifunctional adenosylcobalamin biosynthesis protein
KeywordsTRANSFERASE / Bifunctional adenosylcobalamin biosynthesis protein / adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase / CobU / Methylocapsa palsarum / adenosylcobinamide-phosphate
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
DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / Bifunctional adenosylcobalamin biosynthesis protein
Similarity search - Component
Biological speciesMethylocapsa palsarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.921 Å
AuthorsNam, Y. / Do, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other governmentKIMST 20200610 Korea, Republic Of
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: A structure-based mechanism of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (MpaCobU) from Methylocapsa palsarum.
Authors: Nam, Y. / Ahn, Y.Y. / Kim, B.M. / Kim, K. / Lee, J.H. / Do, H.
History
DepositionMar 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional adenosylcobalamin biosynthesis protein
B: Bifunctional adenosylcobalamin biosynthesis protein
C: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2976
Polymers60,2373
Non-polymers1,0603
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, analytical ultracentrifugation assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.920, 73.960, 130.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional adenosylcobalamin biosynthesis protein


Mass: 20078.975 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylocapsa palsarum (bacteria) / Gene: SAMN05444581_106172 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1I3YTB1, adenosylcobinamide kinase, adenosylcobinamide-phosphate guanylyltransferase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: .2 M ammonium chloride, pH 6.3 and 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→28.212 Å / Num. obs: 41759 / % possible obs: 99.1 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 34
Reflection shellResolution: 1.92→1.97 Å / Num. unique obs: 46479 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.921→28.212 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.216 / SU B: 4.333 / SU ML: 0.126 / Average fsc free: 0.8853 / Average fsc work: 0.9049 / Cross valid method: FREE R-VALUE / ESU R: 0.191 / ESU R Free: 0.176
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2714 2073 4.964 %
Rwork0.2207 39684 -
all0.223 --
obs-41757 99.089 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.318 Å2
Baniso -1Baniso -2Baniso -3
1--0.005 Å2-0 Å2-0 Å2
2---0.002 Å20 Å2
3---0.007 Å2
Refinement stepCycle: LAST / Resolution: 1.921→28.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 65 331 4337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134069
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143998
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.6645530
X-RAY DIFFRACTIONr_angle_other_deg1.3111.5879138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9235516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27619.598224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29215665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1211551
X-RAY DIFFRACTIONr_chiral_restr0.0760.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02963
X-RAY DIFFRACTIONr_nbd_refined0.1990.2750
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23645
X-RAY DIFFRACTIONr_nbtor_refined0.150.21951
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0220.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0570.212
X-RAY DIFFRACTIONr_nbd_other0.1610.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.213
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0590.21
X-RAY DIFFRACTIONr_mcbond_it2.2622.6392079
X-RAY DIFFRACTIONr_mcbond_other2.262.6382078
X-RAY DIFFRACTIONr_mcangle_it3.3433.9412590
X-RAY DIFFRACTIONr_mcangle_other3.3433.9412591
X-RAY DIFFRACTIONr_scbond_it2.9513.1011990
X-RAY DIFFRACTIONr_scbond_other2.8963.0971983
X-RAY DIFFRACTIONr_scangle_it4.5284.5012940
X-RAY DIFFRACTIONr_scangle_other4.4914.4952928
X-RAY DIFFRACTIONr_lrange_it6.32531.9134391
X-RAY DIFFRACTIONr_lrange_other6.30231.7524330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.921-1.970.4261230.2772736X-RAY DIFFRACTION93.1877
1.97-2.0240.2841410.2282852X-RAY DIFFRACTION100
2.024-2.0830.3271340.212774X-RAY DIFFRACTION99.9656
2.083-2.1470.271460.2192679X-RAY DIFFRACTION100
2.147-2.2170.3091310.2472609X-RAY DIFFRACTION100
2.217-2.2950.4851260.4212395X-RAY DIFFRACTION94.4549
2.295-2.3820.2671250.2072442X-RAY DIFFRACTION100
2.382-2.4790.31300.2052336X-RAY DIFFRACTION100
2.479-2.5890.2771220.2112272X-RAY DIFFRACTION100
2.589-2.7150.291190.2132152X-RAY DIFFRACTION100
2.715-2.8610.251090.2082069X-RAY DIFFRACTION100
2.861-3.0350.2611150.2091932X-RAY DIFFRACTION100
3.035-3.2440.256850.2071870X-RAY DIFFRACTION100
3.244-3.5030.263780.221748X-RAY DIFFRACTION100
3.503-3.8360.274750.2141600X-RAY DIFFRACTION99.8807
3.836-4.2870.199810.1861450X-RAY DIFFRACTION99.8044
4.287-4.9470.219790.171280X-RAY DIFFRACTION100
4.947-6.050.267750.221089X-RAY DIFFRACTION100
6.05-8.5190.256510.213884X-RAY DIFFRACTION100
8.519-28.2120.158280.202515X-RAY DIFFRACTION96.2766

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