[English] 日本語
Yorodumi
- PDB-2e20: Crystal structure of Salmonella typhimurium propionate kinase (Td... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2.0E+20
TitleCrystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A)
ComponentsPropionate Kinase
KeywordsTRANSFERASE / Propionate kinase / TdcD / Native / Acetate kinase / Nucleotide / Ap4A / ADP / ATP / AMPPNP
Function / homology
Function and homology information


propionate kinase / propionate kinase activity / L-threonine catabolic process to propionate / acetate kinase activity / acetate metabolic process / phosphorylation / ATP binding / metal ion binding / cytosol
Similarity search - Function
Propionate kinase / Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 ...Propionate kinase / Acetate and butyrate kinases family signature 2. / Acetate/propionate kinase / Aliphatic acid kinase, short-chain, conserved site / Acetate and butyrate kinases family signature 1. / Aliphatic acid kinase, short-chain / Acetokinase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Propionate kinase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsSimanshu, D.K. / Savithri, H.S. / Murthy, M.R.N.
Citation
Journal: Proteins / Year: 2008
Title: Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity.
Authors: Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.N.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily
Authors: Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.
#2: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of propionate kinase (TdcD) from Salmonella typhimurium
Authors: Simanshu, D.K. / Murthy, M.R.
History
DepositionNov 4, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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: Propionate Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1453
Polymers45,2461
Non-polymers8982
Water2,738152
1
A: Propionate Kinase
hetero molecules

A: Propionate Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2906
Polymers90,4932
Non-polymers1,7974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9370 Å2
ΔGint-37 kcal/mol
Surface area28230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.560, 110.560, 66.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

21A-491-

HOH

-
Components

#1: Protein Propionate Kinase /


Mass: 45246.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: IFO 12529 / Gene: TdcD / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O06961, propionate kinase
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Ap4A


Mass: 836.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 45% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), 100mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 23, 2006 / Details: Osmic mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 18755 / % possible obs: 99.2 % / Redundancy: 31.48 % / Biso Wilson estimate: 58.02 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 22.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.05 / Num. unique all: 1775 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1X3M

1x3m


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.096 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.388 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25193 945 5.1 %RANDOM
Rwork0.19943 ---
obs0.20194 17574 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.022 Å2
Baniso -1Baniso -2Baniso -3
1-2.98 Å21.49 Å20 Å2
2--2.98 Å20 Å2
3----4.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2938 0 57 152 3147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213051
X-RAY DIFFRACTIONr_bond_other_d0.0010.021959
X-RAY DIFFRACTIONr_angle_refined_deg1.1451.9714155
X-RAY DIFFRACTIONr_angle_other_deg0.8834777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8595393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52223.571126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00615474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3391521
X-RAY DIFFRACTIONr_chiral_restr0.0630.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02614
X-RAY DIFFRACTIONr_nbd_refined0.1920.2672
X-RAY DIFFRACTIONr_nbd_other0.1850.22128
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21498
X-RAY DIFFRACTIONr_nbtor_other0.0840.21581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2155
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0670.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7051.52509
X-RAY DIFFRACTIONr_mcbond_other0.0751.5811
X-RAY DIFFRACTIONr_mcangle_it0.78123097
X-RAY DIFFRACTIONr_scbond_it1.0731252
X-RAY DIFFRACTIONr_scangle_it1.6134.51058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 64 -
Rwork0.267 1213 -
obs--94.31 %

+
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