[English] 日本語
Yorodumi
- PDB-3wlx: Crystal structure of low-specificity L-threonine aldolase from Es... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wlx
TitleCrystal structure of low-specificity L-threonine aldolase from Escherichia coli
ComponentsLow specificity L-threonine aldolase
KeywordsLYASE / Threonine aldolase / Low specificity / Pyridoxal-5'-phosphate / stereoselectivity
Function / homology
Function and homology information


phenylserine aldolase activity / low-specificity L-threonine aldolase / L-allo-threonine aldolase activity / threonine catabolic process / glycine biosynthetic process / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
Low specificity L-threonine aldolase / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / 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 ...Low specificity L-threonine aldolase / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / 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
Chem-PLG / Low specificity L-threonine aldolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsQin, H.-M. / Imai, F.L. / Miyakawa, T. / Kataoka, M. / Okai, M. / Hou, F. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M.
CitationJournal: To be Published
Title: Structure analysis of L-threonine aldolase from Escherichia coli unravels the low-specificity and thermostability
Authors: Qin, H.-M. / Imai, F.L. / Miyakawa, T. / Kataoka, M. / Okai, M. / Ohtsuka, J. / Hou, F. / Nagata, K. / Shimizu, S. / Tanokura, M.
History
DepositionNov 15, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
B: Low specificity L-threonine aldolase
A: Low specificity L-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6904
Polymers73,0772
Non-polymers6122
Water4,053225
1
B: Low specificity L-threonine aldolase
A: Low specificity L-threonine aldolase
hetero molecules

B: Low specificity L-threonine aldolase
A: Low specificity L-threonine aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,3808
Polymers146,1554
Non-polymers1,2254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area14700 Å2
ΔGint-53 kcal/mol
Surface area42860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.730, 100.340, 174.620
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
11CHAIN A
21CHAIN B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PLG / End label comp-ID: PLG / Auth seq-ID: 1 - 401 / Label seq-ID: 1

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN AAB - D
2CHAIN BBA - C

-
Components

#1: Protein Low specificity L-threonine aldolase / Low specificity L-TA


Mass: 36538.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0870, JW0854, ltaE, ybjU / Plasmid: PET-28A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3)
References: UniProt: P75823, low-specificity L-threonine aldolase
#2: Chemical ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M calcium chloride, 0.1M HEPES pH 7.5, 28% (v/v) PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→20 Å / Num. obs: 23010 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 19.27 Å2 / Rsym value: 0.05
Reflection shellHighest resolution: 2.51 Å / Redundancy: 7 % / Rsym value: 0.103 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→19.681 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8521 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.71 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 1181 5.13 %RANDOM
Rwork0.1829 ---
obs0.1855 23007 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.14 Å2 / Biso mean: 28.1 Å2 / Biso min: 9.97 Å2
Refinement stepCycle: LAST / Resolution: 2.51→19.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5038 0 40 225 5303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035166
X-RAY DIFFRACTIONf_angle_d0.7247011
X-RAY DIFFRACTIONf_dihedral_angle_d14.4751873
X-RAY DIFFRACTIONf_chiral_restr0.026791
X-RAY DIFFRACTIONf_plane_restr0.003918
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2865X-RAY DIFFRACTION11.162TORSIONAL
12B2865X-RAY DIFFRACTION11.162TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5092-2.62320.27131470.19552615276297
2.6232-2.76110.23591460.190227002846100
2.7611-2.93360.28811470.194926892836100
2.9336-3.15930.25991470.203727372884100
3.1593-3.47560.23891510.189627102861100
3.4756-3.9750.22281470.166327482895100
3.975-4.99450.17861660.157427392905100
4.9945-19.68120.23681300.193228883018100

+
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