[English] 日本語
Yorodumi
- PDB-1un8: Crystal structure of the dihydroxyacetone kinase of C. freundii (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1un8
TitleCrystal structure of the dihydroxyacetone kinase of C. freundii (native form)
ComponentsDIHYDROXYACETONE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


glycerone kinase / anaerobic glycerol catabolic process / glycerone kinase activity / lipid binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Dihydroxyacetone kinase / DhaL domain / DhaK domain / Dak1 domain / DhaK domain profile. / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 ...Dihydroxyacetone kinase / DhaL domain / DhaK domain / Dak1 domain / DhaK domain profile. / DhaL domain / DhaL domain superfamily / DAK2 domain / DhaL domain profile. / Dak2 / : / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Chem-MYY / Dihydroxyacetone kinase
Similarity search - Component
Biological speciesCITROBACTER FREUNDII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSiebold, C. / Arnold, I. / Garcia-Alles, L.F. / Baumann, U. / Erni, B.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of the Citrobacter Freundii Dihydroxyacetone Kinase Reveals an Eight-Stranded Alpha-Helical Barrel ATP-Binding Domain
Authors: Siebold, C. / Arnold, I. / Garcia-Alles, L.F. / Baumann, U. / Erni, B.
History
DepositionSep 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROXYACETONE KINASE
B: DIHYDROXYACETONE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,2274
Polymers115,9862
Non-polymers1,2422
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-79.9 kcal/mol
Surface area39870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.440, 124.590, 237.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLNGLN1AA1 - 3511 - 351
211METMETGLNGLN1BB1 - 3511 - 351
121SERSERALAALA1AA2 - 5172 - 517
221SERSERALAALA1BB2 - 5172 - 517
112GLUGLUGLUGLU2AA526 - 550526 - 550
212GLUGLUGLUGLU2BB526 - 550526 - 550

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (0.05306, 0.9985, -0.01375), (0.99849, -0.05325, -0.01346), (-0.01417, -0.01302, -0.99981)
Vector: -61.43323, 68.94242, 297.64081)

-
Components

#1: Protein DIHYDROXYACETONE KINASE / GLYCERONE KINASE / DHA KINASE


Mass: 57992.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CITROBACTER FREUNDII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P45510, glycerone kinase
#2: Chemical ChemComp-MYY / (2R)-3-(PHOSPHONOOXY)-2-(TETRADECANOYLOXY)PROPYL PALMITATE


Mass: 620.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H65O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130-50 mg/mlprotein1drop
25 mMHEPES1droppH7.5
32 mMdithiothreitol1drop
4100 mMHEPES1reservoirpH7.3
550 mM1reservoirNaCl
69 %(w/v)PEG30001reservoir
725 %(v/v)glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 50187 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.4
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 83.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 9.1

-
Processing

SoftwareName: REFMAC / Version: 5.1.19 / Classification: refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.92 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.64 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES 518 - 525 WERE NOT VISIBLE IN ELECTRON DENSITY. N-TERMINAL MET WAS MODELLED AS ALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3976 7.9 %RANDOM
Rwork0.196 ---
obs0.2 46053 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.42 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å20 Å2
2--7.13 Å20 Å2
3----4.73 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7976 0 84 211 8271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218110
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.96811016
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.55251080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.21318
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.026040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2620.24203
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7942.55370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9723.58542
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1313.52740
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4474.52474
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A6348tight positional0.090.05
12B6348tight positional0.090.05
21A180tight positional0.080.05
22B180tight positional0.080.05
11A6348tight thermal0.340.5
12B6348tight thermal0.340.5
21A180tight thermal0.460.5
22B180tight thermal0.460.5
LS refinement shellResolution: 2.5→2.55 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.405 187
Rwork0.313 2253
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7181-0.12440.13420.17150.0122.36590.0931-0.08660.1092-0.13690.0269-0.0389-0.21290.0842-0.120.3295-0.0930.11050.0365-0.00450.381128.41485.468135.058
23.1186-0.5212-1.20931.20410.61195.42780.07610.1626-0.08970.0663-0.0249-0.05320.07810.1744-0.05120.2188-0.0255-0.01220.2744-0.08120.253620.07877.728195.249
30.3044-0.05190.29450.1646-0.06252.71250.021-0.3160.08390.00420.0538-0.0388-0.5021-0.1274-0.07480.3417-0.06010.08350.2638-0.06990.371723.55890.956161.049
40.80590.33560.17913.50250.36272.42110.12880.1571-0.0395-0.4109-0.08250.2806-0.16980.0344-0.04630.35590.16310.05010.14410.08940.314314.56582.215101.088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 351
2X-RAY DIFFRACTION2A352 - 550
3X-RAY DIFFRACTION3B1 - 351
4X-RAY DIFFRACTION4B352 - 550
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.245 / Rfactor Rwork: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.432

+
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