[English] 日本語
Yorodumi
- PDB-1cbu: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cbu
TitleADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE (COBU) FROM SALMONELLA TYPHIMURIUM
ComponentsADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
KeywordsCOBALAMIN BIOSYNTHESIS / ADENOSYLCOBINAMIDE / KINASE / ATPASE / GUANYLYLTRANSFERASE / SALMONELLA TYPHIMURIUM / TRANSFERASE / COENZYME B12
Function / homology
Function and homology information


adenosylcobinamide kinase / adenosylcobinamide kinase (GTP-specific) activity / adenosylcobinamide kinase (ATP-specific) activity / adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / phosphorylation / GTP binding / ATP binding
Similarity search - Function
Cobinamide kinase/cobinamide phosphate guanyltransferase / Cobinamide kinase / cobinamide phosphate guanyltransferase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional adenosylcobalamin biosynthesis protein CobU
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsThompson, T.B. / Thomas, M.G. / Escalante-Semerena, J.C. / Rayment, I.
Citation
Journal: Biochemistry / Year: 1998
Title: Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 A resolution,.
Authors: Thompson, T.B. / Thomas, M.G. / Escalante-Semerena, J.C. / Rayment, I.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: Purification and Characterization of the Bifunctional Cobu Enzyme of Salmonella Typhimurium Lt2. Evidence for a Cobu-Gmp Intermediate
Authors: O'Toole, G.A. / Escalante-Semerena, J.C.
History
DepositionMar 12, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
B: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
C: ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6726
Polymers59,3843
Non-polymers2883
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-93 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.400, 114.400, 106.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.34327, 0.56648, 0.74918), (-0.55671, -0.51971, 0.64805), (0.75647, -0.63953, 0.13697)-43.18497, 15.23066, 49.20813
2given(0.35818, -0.56417, 0.74392), (0.59147, -0.47939, -0.64834), (0.72241, 0.67223, 0.16198)-13.33835, 62.20041, 14.04711

-
Components

#1: Protein ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE


Mass: 19794.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): LT2 / References: UniProt: Q05599
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 50 %
Crystal growMethod: microbatch / pH: 5.5
Details: PROTEIN WAS CRYSTALLIZED BY MICRO BATCH FROM 6% PEG 3350, 200 MM NACL AND 50 MM SUCCINATE, PH 5.5 AT 4 C., micro batch
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 %PEG335011
2200 mM11NaCl
350 mMsuccinate11
45-8 mg/mlprotein11

-
Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Sep 1, 1997 / Details: SIEMENS GOBEL FOCUSING OPTICS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 24136 / % possible obs: 88.5 % / Observed criterion σ(I): 0.33 / Redundancy: 3 % / Biso Wilson estimate: 46.9 Å2 / Rsym value: 0.043 / Net I/σ(I): 16
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.21 / % possible all: 64.4
Reflection
*PLUS
Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 64.4 % / Rmerge(I) obs: 0.21

-
Processing

Software
NameVersionClassification
HEAVYmodel building
TNT4Crefinement
XDSdata reduction
XCALIBREdata scaling
HEAVYphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→20 Å / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.198 26109 -
obs-24136 88.5 %
Solvent computationSolvent model: TNT / Bsol: 740 Å2 / ksol: 0.97 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4117 0 15 202 4334
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01563711
X-RAY DIFFRACTIONt_angle_deg2.0784152
X-RAY DIFFRACTIONt_dihedral_angle_d18.541470
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle00
X-RAY DIFFRACTIONt_trig_c_planes0.0041118
X-RAY DIFFRACTIONt_gen_planes0.005115316
X-RAY DIFFRACTIONt_it042250
X-RAY DIFFRACTIONt_nbd0.0414610
Software
*PLUS
Name: TNT / Version: 4C / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.50
X-RAY DIFFRACTIONt_plane_restr0.00516

+
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