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

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Basic information

Entry
Database: PDB / ID: 8yes
TitleCrystal structure of adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase complexed with adenosylcobinamide-phosphate
ComponentsBifunctional adenosylcobalamin biosynthesis protein
KeywordsTRANSFERASE / Biosynthesis of cobalamin / kinase / guanylyltransferase / X-ray crystalligraphy / Methylocapsa palsarum
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
5'-DEOXYADENOSINE / COBALAMIN / PHOSPHATE ION / Bifunctional adenosylcobalamin biosynthesis protein
Similarity search - Component
Biological speciesMethylocapsa palsarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNam, Y. / Do, H.
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
DepositionFeb 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 2.0Jan 15, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_ref / struct_ref_seq
Item: _atom_site.label_entity_id / _cell.Z_PDB ..._atom_site.label_entity_id / _cell.Z_PDB / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end

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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
D: Bifunctional adenosylcobalamin biosynthesis protein
E: Bifunctional adenosylcobalamin biosynthesis protein
F: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,11832
Polymers116,2996
Non-polymers10,81926
Water48627
1
A: Bifunctional adenosylcobalamin biosynthesis protein
B: Bifunctional adenosylcobalamin biosynthesis protein
C: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,65417
Polymers58,1503
Non-polymers5,50514
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-94 kcal/mol
Surface area22520 Å2
MethodPISA
2
D: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules

E: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules

F: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,46415
Polymers58,1503
Non-polymers5,31512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
crystal symmetry operation2_655x+1,-y,-z1
Buried area12420 Å2
ΔGint-89 kcal/mol
Surface area22720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.213, 102.922, 129.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Bifunctional adenosylcobalamin biosynthesis protein


Mass: 19383.207 Da / Num. of mol.: 6
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-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Sodium Chloride, 0.1 M Bis-Tris: HCl, pH 6.5, 1.3 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97942 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.6→47.964 Å / Num. obs: 41344 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 15.4
Reflection shellResolution: 2.6→2.71 Å / Num. unique obs: 4610 / 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: 2.6→47.964 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.72 / SU ML: 0.282 / Cross valid method: FREE R-VALUE / ESU R: 0.741 / ESU R Free: 0.33
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2633 2119 5.13 %
Rwork0.1931 39185 -
all0.197 --
obs-41304 99.761 %
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: 66.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0 Å2-0 Å2
2---0.013 Å20 Å2
3---0.015 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8116 0 610 27 8753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138894
X-RAY DIFFRACTIONr_bond_other_d0.0010.0148670
X-RAY DIFFRACTIONr_angle_refined_deg2.181.72912230
X-RAY DIFFRACTIONr_angle_other_deg1.2231.64719750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.82451064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49319.617470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.774151382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.10215108
X-RAY DIFFRACTIONr_chiral_restr0.1110.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210036
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022136
X-RAY DIFFRACTIONr_nbd_refined0.2030.21515
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.28109
X-RAY DIFFRACTIONr_nbtor_refined0.1530.24067
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.24649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2131
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.243
X-RAY DIFFRACTIONr_nbd_other0.2250.2182
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.28
X-RAY DIFFRACTIONr_mcbond_it5.6466.7684274
X-RAY DIFFRACTIONr_mcbond_other5.6416.7684273
X-RAY DIFFRACTIONr_mcangle_it8.14510.1435332
X-RAY DIFFRACTIONr_mcangle_other8.14510.1455333
X-RAY DIFFRACTIONr_scbond_it6.3967.3184619
X-RAY DIFFRACTIONr_scbond_other6.3667.3174564
X-RAY DIFFRACTIONr_scangle_it9.38610.6966897
X-RAY DIFFRACTIONr_scangle_other9.3710.6896814
X-RAY DIFFRACTIONr_lrange_it13.676129.00633680
X-RAY DIFFRACTIONr_lrange_other13.675129.00533681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.3141460.2852851X-RAY DIFFRACTION99.8667
2.668-2.7410.3431370.2852792X-RAY DIFFRACTION99.7956
2.741-2.820.3721560.2632712X-RAY DIFFRACTION99.7565
2.82-2.9070.3161280.2482646X-RAY DIFFRACTION99.856
2.907-3.0020.31470.2322557X-RAY DIFFRACTION99.8892
3.002-3.1070.2941310.2252492X-RAY DIFFRACTION99.8858
3.107-3.2240.3111310.2242368X-RAY DIFFRACTION99.7207
3.224-3.3560.2821420.222280X-RAY DIFFRACTION99.9175
3.356-3.5050.2981270.1952214X-RAY DIFFRACTION99.872
3.505-3.6760.281160.1932141X-RAY DIFFRACTION99.8231
3.676-3.8740.258970.1962024X-RAY DIFFRACTION99.9529
3.874-4.1090.268970.1821931X-RAY DIFFRACTION99.7541
4.109-4.3920.216970.151799X-RAY DIFFRACTION99.8946
4.392-4.7430.2161220.151668X-RAY DIFFRACTION99.8884
4.743-5.1950.244820.1951551X-RAY DIFFRACTION99.0898
5.195-5.8060.244720.2081428X-RAY DIFFRACTION99.4036
5.806-6.70.298890.2021244X-RAY DIFFRACTION99.925
6.7-8.1970.199450.141101X-RAY DIFFRACTION99.9128
8.197-11.5530.171420.126863X-RAY DIFFRACTION99.3414
11.553-47.9640.364150.239523X-RAY DIFFRACTION97.6406

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