[English] 日本語
Yorodumi
- PDB-8yep: Crystal structure of adenosylcobinamide kinase / adenosylcobinami... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yep
TitleCrystal structure of adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase from Methylocapsa palsarum
ComponentsBifunctional adenosylcobalamin biosynthesis protein
KeywordsTRANSFERASE / Bifunctional adenosylcobalamin biosynthesis protein / adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase / CobU / 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
PHOSPHATE ION / Bifunctional adenosylcobalamin biosynthesis protein
Similarity search - Component
Biological speciesMethylocapsa palsarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionFeb 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)60,7146
Polymers60,4293
Non-polymers2853
Water2,288127
1
A: Bifunctional adenosylcobalamin biosynthesis protein
B: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules

C: Bifunctional adenosylcobalamin biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7146
Polymers60,4293
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area7300 Å2
ΔGint-55 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 104.970, 111.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Bifunctional adenosylcobalamin biosynthesis protein


Mass: 20143.037 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-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.: 127 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.09 M NPS (sodium nitrate, sodium phosphate dibasic, ammonium sulfate), 0.1 M Buffer System 3 (Tris, Bicine (pH 8.5)), and 37.5% of Precipitant Mix 4 (25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350)

-
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: Nov 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.654 Å / Num. obs: 57890 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.1
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 3355 / CC1/2: 1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.654 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.216 / SU B: 4.573 / SU ML: 0.129 / Average fsc free: 0.7883 / Average fsc work: 0.8087 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2565 2794 4.826 %
Rwork0.2218 55096 -
all0.223 --
obs-57890 99.709 %
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: 41.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å2-0 Å20 Å2
2--0.003 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 15 127 3863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133790
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143771
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.6435144
X-RAY DIFFRACTIONr_angle_other_deg1.3081.5768617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1635486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37719.703202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17515623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5041545
X-RAY DIFFRACTIONr_chiral_restr0.0750.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024269
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02893
X-RAY DIFFRACTIONr_nbd_refined0.2020.2660
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23354
X-RAY DIFFRACTIONr_nbtor_refined0.1530.21818
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2152
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.230
X-RAY DIFFRACTIONr_nbd_other0.2120.2115
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.222
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2140.21
X-RAY DIFFRACTIONr_mcbond_it3.4914.0641962
X-RAY DIFFRACTIONr_mcbond_other3.4914.0631961
X-RAY DIFFRACTIONr_mcangle_it4.8856.0692442
X-RAY DIFFRACTIONr_mcangle_other4.8856.0692443
X-RAY DIFFRACTIONr_scbond_it4.2944.6671828
X-RAY DIFFRACTIONr_scbond_other4.2914.6721817
X-RAY DIFFRACTIONr_scangle_it6.316.8032702
X-RAY DIFFRACTIONr_scangle_other6.3146.8082685
X-RAY DIFFRACTIONr_lrange_it7.97548.0113929
X-RAY DIFFRACTIONr_lrange_other7.98447.9723910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.4142250.43955X-RAY DIFFRACTION99.0756
1.847-1.8970.3912280.3743880X-RAY DIFFRACTION99.0596
1.897-1.9520.3841910.3443810X-RAY DIFFRACTION99.5026
1.952-2.0120.3251680.3163710X-RAY DIFFRACTION99.7941
2.012-2.0780.3141720.2933578X-RAY DIFFRACTION99.5751
2.078-2.1510.3172100.2743455X-RAY DIFFRACTION99.7822
2.151-2.2320.3091710.253365X-RAY DIFFRACTION99.8024
2.232-2.3230.2891770.2553261X-RAY DIFFRACTION99.9128
2.323-2.4270.2741500.2323092X-RAY DIFFRACTION100
2.427-2.5450.2621420.2183014X-RAY DIFFRACTION99.9683
2.545-2.6820.2741350.2242865X-RAY DIFFRACTION100
2.682-2.8450.2321250.222707X-RAY DIFFRACTION100
2.845-3.0410.3011190.2162554X-RAY DIFFRACTION99.9252
3.041-3.2840.2411070.2162412X-RAY DIFFRACTION100
3.284-3.5970.2441000.2122201X-RAY DIFFRACTION100
3.597-4.020.217990.1862016X-RAY DIFFRACTION100
4.02-4.640.1961070.1631764X-RAY DIFFRACTION100
4.64-5.6780.227810.1971515X-RAY DIFFRACTION100
5.678-8.0080.234680.2081200X-RAY DIFFRACTION100
8.008-29.6540.202180.197719X-RAY DIFFRACTION96.5924

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more