[English] 日本語
Yorodumi
- PDB-1n3b: Crystal Structure of Dephosphocoenzyme A kinase from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n3b
TitleCrystal Structure of Dephosphocoenzyme A kinase from Escherichia coli
ComponentsDephospho-CoA kinase
KeywordsTRANSFERASE / trimer / P-loop / alpha/beta / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Dephospho-CoA kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsO'Toole, N. / Barbosa, J.A.R.G. / Li, Y. / Hung, L.-W. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Citation
Journal: Protein Sci. / Year: 2003
Title: Crystal Structure of a Trimeric Form of Dephosphocoenzyme A Kinase from Escherichia coli
Authors: O'Toole, N. / Barbosa, J.A.R.G. / Li, Y. / Hung, L.-W. / Matte, A. / Cygler, M.
#1: Journal: J.Struct.Biol. / Year: 2001
Title: Crystal Structure of Dephospho-coenzyme A Kinase from Haemophilus influenzae
Authors: Oblomova, G. / Teplyakov, A. / Bonander, N. / Eisenstein, E. / Howard, A. / Gilliland, G.
#2: Journal: J.Bacteriol. / Year: 2001
Title: Identification of yace (coaE) as the Structural Gene for Dephosphocoenzyme A Kinase in Escherichia coli K-12
Authors: Mishra, P.K. / Park, P.K. / Drueckhammer, D.G.
#3: Journal: J.Mol.Biol. / Year: 1998
Title: The structure of a Trimeric Archael Adenylate Kinase
Authors: Vorhein, C. / Bonisch, H. / Schafer, G. / Schulz, G.E.
#4: Journal: Biochem.J. / Year: 1983
Title: A Bifunctional Enzyme Complex in Coenzyme A Biosynthesis: Purification of Pantetheine Phosphate Adenylyltransferase and Dephospho-CoA Kinase
Authors: Worral, D.M. / Tubbs, P.K.
#5: Journal: Biochem.J. / Year: 2002
Title: Identification and Characterization of the Gene Encoding the Human Adenylyltransferase and Dephosphocoenzyme A Kinase Bifunctional Enzyme
Authors: Aghajanian, S. / Worral, D.M.
History
DepositionOct 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 16, 2014Group: Data collection
Revision 1.4Feb 1, 2017Group: Structure summary
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Dephospho-CoA kinase
B: Dephospho-CoA kinase
C: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,07413
Polymers72,1133
Non-polymers96110
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-165 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.500, 82.410, 76.000
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Dephospho-CoA kinase / Dephosphocoenzyme A kinase


Mass: 24037.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: COAE / Plasmid: pET20b derivative / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3) / References: UniProt: P0A6I9, dephospho-CoA kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, cacodylate buffer, ammonium sulfate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-Cl1droppH7.5
20.2 M1dropNaCl
35 %(v/v)glycerol1drop
410 mMdithiothreitol1drop
59.3 mg/mlprotein1drop
620 %(w/v)PEG80001reservoir
750 mMcacodylate1reservoirpH6.5
80.2 Mammonium sulfate1reservoir
95 %(v/v)glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97957, 0.97941
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 4, 2001 / Details: monochromating crystal
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979571
20.979411
ReflectionResolution: 1.8→40 Å / Num. obs: 59512 / % possible obs: 86.3 % / Redundancy: 6.7 % / Rsym value: 0.065 / Net I/σ(I): 26.1
Reflection shellResolution: 1.81→1.88 Å / Num. unique all: 5096 / Rsym value: 0.439 / % possible all: 74.3
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 56459 / % possible obs: 88.7 % / Num. measured all: 380533 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.87 Å / % possible obs: 71.1 % / Rmerge(I) obs: 0.546

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→40 Å / Isotropic thermal model: isotropic / Cross valid method: Free-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Bulk solvent correction employed. The structure was refined using Friedel's pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5518 4.4 %Random
Rwork0.217 ---
obs-107923 86.8 %-
Displacement parametersBiso mean: 28.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 50 449 5046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_bond_d0.008
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.008

+
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