[English] 日本語
Yorodumi
- PDB-1lkc: Crystal Structure of L-Threonine-O-3-Phosphate Decarboxylase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lkc
TitleCrystal Structure of L-Threonine-O-3-Phosphate Decarboxylase from Salmonella enterica
ComponentsL-threonine-O-3-phosphate decarboxylase
KeywordsLYASE / CobD / L-threonine-O-3-phosphate / 1-amino-2-propanol-phosphate / PLP / decarboxylase / cobalamin
Function / homology
Function and homology information


threonine-phosphate decarboxylase / threonine-phosphate decarboxylase activity / cobalamin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding
Similarity search - Function
L-threonine-O-3-phosphate decarboxylase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...L-threonine-O-3-phosphate decarboxylase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Threonine-phosphate decarboxylase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsCheong, C.G. / Bauer, C.B. / Brushaber, K.R. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: Biochemistry / Year: 2002
Title: Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica.
Authors: Cheong, C.G. / Bauer, C.B. / Brushaber, K.R. / Escalante-Semerena, J.C. / Rayment, I.
History
DepositionApr 24, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionMay 1, 2002ID: 1KUS
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Remark 999SEQUENCE According to the authors, the GenBank entry is in error because the original DNA sequence ...SEQUENCE According to the authors, the GenBank entry is in error because the original DNA sequence had some errors. The electron density also supports it. The new sequence is Gln25, Ser30, Val42, Arg44 and Ala45. Arg44 lacks side chain density. The organism name in this GenBank entry is Salmonella typhimurium. Salmonella typhimurium has been changed to Salmonella enterica. Therefore, the two names are same.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-threonine-O-3-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3165
Polymers40,8501
Non-polymers4664
Water3,873215
1
A: L-threonine-O-3-phosphate decarboxylase
hetero molecules

A: L-threonine-O-3-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,63210
Polymers81,7002
Non-polymers9328
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
Buried area6210 Å2
ΔGint-33 kcal/mol
Surface area26350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.960, 101.550, 117.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1324-

HOH

-
Components

#1: Protein L-threonine-O-3-phosphate decarboxylase / CobD


Mass: 40849.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: cobD / Production host: Escherichia coli (E. coli) / References: UniProt: P97084
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium phosphate, KCl, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMHEPES1droppH7.0
2150 mM1dropNaCl
32 mMdithiothreitol1drop
410 mMprotein1drop
51.5 Mammonium phosphate1reservoir
620 mM1reservoirKCl
75 %glycerol1reservoir
850 mMBis-Tris propane1reservoirpH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.94645, 0.97915, 0.97926, 1.0205
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979151
30.979261
41.02051
ReflectionResolution: 1.8→30 Å / Num. obs: 37844 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 37
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.243 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 100 %

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1899 -random
Rwork0.203 ---
obs-37844 99.6 %-
Solvent computationBsol: 56.0846 Å2 / ksol: 0.362921 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.597 Å20 Å20 Å2
2--0.128 Å20 Å2
3---8.469 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 28 215 2981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_mcbond_it3.0361.5
X-RAY DIFFRACTIONc_scbond_it4.7792
X-RAY DIFFRACTIONc_mcangle_it3.6112
X-RAY DIFFRACTIONc_scangle_it6.212.5
LS refinement shellResolution: 1.8→1.86 Å
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3pi.parapi.topo
X-RAY DIFFRACTION4plplys.paraplplys.topo
Refinement
*PLUS
Rfactor obs: 0.201 / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.69
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg14.3
X-RAY DIFFRACTIONc_plane_restr0.014
LS refinement shell
*PLUS
Highest resolution: 1.8 Å

+
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://pdbjlvh1.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