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- PDB-8yk8: adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltr... -

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Basic information

Entry
Database: PDB / ID: 8yk8
Titleadenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase -C91S
ComponentsBifunctional adenosylcobalamin biosynthesis protein
KeywordsTRANSFERASE / C91S mutant / phosphorylation / guanylylation / ping-pong mechanism / ternary complex mechanism
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
PHOSPHATE ION / Bifunctional adenosylcobalamin biosynthesis protein
Similarity search - Component
Biological speciesMethylocapsa palsarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDo, H. / Nam, Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privateKIMST 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3644
Polymers20,0791
Non-polymers2853
Water1,56787
1
A: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules

A: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules

A: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,09212
Polymers60,2373
Non-polymers8559
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Unit cell
Length a, b, c (Å)60.970, 60.970, 73.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Bifunctional adenosylcobalamin biosynthesis protein


Mass: 20078.975 Da / Num. of mol.: 1
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.1 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.49M Sodium phosphate monobasic monohydrate, 0.91M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→28.169 Å / Num. obs: 24858 / % possible obs: 100 % / Redundancy: 20.3 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.6
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1253 / 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: 1.5→28.169 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.416 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2389 1273 5.126 %
Rwork0.2049 23561 -
all0.207 --
obs-24834 99.968 %
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: 23.346 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1316 0 15 87 1418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131348
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141330
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.6371829
X-RAY DIFFRACTIONr_angle_other_deg1.5411.5793041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25119.86373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34215223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6461516
X-RAY DIFFRACTIONr_chiral_restr0.10.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021515
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02313
X-RAY DIFFRACTIONr_nbd_refined0.2250.2255
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21219
X-RAY DIFFRACTIONr_nbtor_refined0.1640.2676
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.211
X-RAY DIFFRACTIONr_nbd_other0.230.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.212
X-RAY DIFFRACTIONr_mcbond_it1.9882.198694
X-RAY DIFFRACTIONr_mcbond_other1.9772.196693
X-RAY DIFFRACTIONr_mcangle_it2.7373.285864
X-RAY DIFFRACTIONr_mcangle_other2.7383.286865
X-RAY DIFFRACTIONr_scbond_it3.2282.664654
X-RAY DIFFRACTIONr_scbond_other3.2412.669643
X-RAY DIFFRACTIONr_scangle_it4.5413.851965
X-RAY DIFFRACTIONr_scangle_other4.5593.855948
X-RAY DIFFRACTIONr_lrange_it5.85727.5251452
X-RAY DIFFRACTIONr_lrange_other5.8527.3121436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.28750.2331751X-RAY DIFFRACTION99.8906
1.539-1.5810.2841080.2221681X-RAY DIFFRACTION100
1.581-1.6270.259940.2091642X-RAY DIFFRACTION100
1.627-1.6770.212910.1911593X-RAY DIFFRACTION100
1.677-1.7320.229530.2161585X-RAY DIFFRACTION100
1.732-1.7930.266980.2091484X-RAY DIFFRACTION100
1.793-1.860.228750.2051435X-RAY DIFFRACTION100
1.86-1.9360.254840.211380X-RAY DIFFRACTION100
1.936-2.0220.249660.2131348X-RAY DIFFRACTION100
2.022-2.120.229760.2091278X-RAY DIFFRACTION100
2.12-2.2350.241620.211208X-RAY DIFFRACTION100
2.235-2.370.231570.2031170X-RAY DIFFRACTION100
2.37-2.5340.288490.1981091X-RAY DIFFRACTION100
2.534-2.7360.261510.2091015X-RAY DIFFRACTION100
2.736-2.9960.22530.222919X-RAY DIFFRACTION100
2.996-3.3490.263420.202849X-RAY DIFFRACTION100
3.349-3.8640.186400.196743X-RAY DIFFRACTION100
3.864-4.7260.236520.185619X-RAY DIFFRACTION100
4.726-6.6570.243310.209493X-RAY DIFFRACTION100
6.657-28.1690.234160.197277X-RAY DIFFRACTION97.9933

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