[English] 日本語
Yorodumi
- PDB-4rjy: Crystal structure of E. coli L-Threonine Aldolase in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rjy
TitleCrystal structure of E. coli L-Threonine Aldolase in complex with a non-covalently uncleaved bound L-serine substrate
ComponentsLow specificity L-threonine aldolase
KeywordsLYASE / Pyridoxal-5-phosphate / threonine aldolase / aldimine / catalytic mechanism / retro-aldol cleavage / PLP-dependent enzymes
Function / homologyAspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta / SERINE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSafo, M.K. / Chowdhury, N. / Gandhi, A.K.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Molecular basis of E. colil-threonine aldolase catalytic inactivation at low pH.
Authors: Remesh, S.G. / Ghatge, M.S. / Ahmed, M.H. / Musayev, F.N. / Gandhi, A. / Chowdhury, N. / di Salvo, M.L. / Kellogg, G.E. / Contestabile, R. / Schirch, V. / Safo, M.K.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Low specificity L-threonine aldolase
B: Low specificity L-threonine aldolase
C: Low specificity L-threonine aldolase
D: Low specificity L-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,58614
Polymers147,0284
Non-polymers55810
Water15,331851
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15680 Å2
ΔGint-120 kcal/mol
Surface area43890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 104.880, 84.910
Angle α, β, γ (deg.)90.00, 92.49, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Low specificity L-threonine aldolase


Mass: 36756.883 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: KTE79 / Gene: A1UU_02790 / Production host: Escherichia coli (E. coli) / References: UniProt: L4EJM2
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / 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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Freshly dialyzed eTA (22 mg/mL in 20 mM potassium phosphate, pH 7.0) was incubated with L-serine (6.25 mM), precipitant solution contains 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 20% ...Details: Freshly dialyzed eTA (22 mg/mL in 20 mM potassium phosphate, pH 7.0) was incubated with L-serine (6.25 mM), precipitant solution contains 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 20% v/v 2-propoanol, 20% v/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5417 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 22, 2011
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.1→32.8 Å / Num. obs: 77165 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.91 % / Rmerge(I) obs: 0.093 / Χ2: 0.87 / Net I/σ(I): 8.4 / Scaling rejects: 24943
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.1-2.182.770.2683.82293874580.995.4
2.18-2.262.860.2544.12441276910.998.1
2.26-2.372.90.2464.22460477020.9198.2
2.37-2.492.870.2284.52482077740.998.5
2.49-2.652.90.1975.12486877210.8998.6
2.65-2.852.90.1695.72519677260.998.4
2.85-3.142.920.136.92547277870.8898.8
3.14-3.592.930.08410.22547577290.8698.3
3.59-4.522.980.05116.42558877440.8197.5
4.52-32.83.040.03921.12605178330.7597.9

-
Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata reduction
CNSrefinement
PDB_EXTRACT3.15data extraction
CrystalCleardata collection
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 3871 4.9 %random
Rwork0.2125 ---
obs0.2787 76865 97.6 %-
all-77165 --
Solvent computationBsol: 78.7595 Å2
Displacement parametersBiso max: 113.59 Å2 / Biso mean: 27.2876 Å2 / Biso min: 1.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.873 Å20 Å20.122 Å2
2---3.987 Å20 Å2
3---1.114 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10252 0 34 851 11137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.507
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3llp.par
X-RAY DIFFRACTION4llp-patch.par
X-RAY DIFFRACTION5sen.par

+
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