[English] 日本語
Yorodumi
- PDB-9d2q: Crystal structure of E. coli Threonine dehydratase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9d2q
TitleCrystal structure of E. coli Threonine dehydratase
ComponentsL-threonine dehydratase biosynthetic IlvA
KeywordsLYASE / Escherichia coli / threonine dehydratase / IlvA / isoleucine / branched-chain amino acids / regulation / allostery / PLP
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / threonine metabolic process / branched-chain amino acid biosynthetic process / isoleucine biosynthetic process / amino acid binding / pyridoxal phosphate binding
Similarity search - Function
Threonine dehydratase, biosynthetic / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Pyridoxal-phosphate dependent enzyme ...Threonine dehydratase, biosynthetic / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / L-threonine dehydratase biosynthetic IlvA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsYun, M. / Rock, C.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
CitationJournal: Biochemistry / Year: 2025
Title: Isoleucine Binding and Regulation of Escherichia coli and Staphylococcus aureus Threonine Dehydratase (IlvA).
Authors: Yun, M.K. / Subramanian, C. / Miller, K. / Jackson, P. / Radka, C.D. / Rock, C.O.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-threonine dehydratase biosynthetic IlvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1966
Polymers58,5311
Non-polymers6655
Water4,107228
1
A: L-threonine dehydratase biosynthetic IlvA
hetero molecules

A: L-threonine dehydratase biosynthetic IlvA
hetero molecules

A: L-threonine dehydratase biosynthetic IlvA
hetero molecules

A: L-threonine dehydratase biosynthetic IlvA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,78424
Polymers234,1254
Non-polymers2,65920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)80.018, 93.099, 161.545
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-907-

HOH

-
Components

#1: Protein L-threonine dehydratase biosynthetic IlvA / Threonine deaminase


Mass: 58531.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SCHIFF BASE LINKAGE BETWEEN LYS 62 AND PLP / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ilvA, b3772, JW3745 / Production host: Escherichia coli (E. coli) / References: UniProt: P04968, threonine ammonia-lyase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES, magnesium chloride, PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→60.68 Å / Num. obs: 50171 / % possible obs: 99.7 % / Redundancy: 13.4 % / Biso Wilson estimate: 36.32 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.127 / Net I/σ(I): 10
Reflection shellResolution: 1.87→1.9 Å / Rmerge(I) obs: 3.44 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2340 / CC1/2: 0.719

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→60.68 Å / SU ML: 0.2166 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 24.0098 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2017 2000 3.99 %
Rwork0.1758 48144 -
obs0.1769 50144 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.67 Å2
Refinement stepCycle: LAST / Resolution: 1.87→60.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 58 228 4082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583925
X-RAY DIFFRACTIONf_angle_d0.79695299
X-RAY DIFFRACTIONf_chiral_restr0.0521581
X-RAY DIFFRACTIONf_plane_restr0.0051690
X-RAY DIFFRACTIONf_dihedral_angle_d11.352343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.33681410.31293398X-RAY DIFFRACTION99.92
1.92-1.970.30651400.2843360X-RAY DIFFRACTION99.91
1.97-2.030.26571430.24473451X-RAY DIFFRACTION99.94
2.03-2.090.25381400.22023360X-RAY DIFFRACTION99.91
2.09-2.170.27451420.20513419X-RAY DIFFRACTION99.94
2.17-2.250.24421420.19833428X-RAY DIFFRACTION99.97
2.25-2.360.21321420.18873417X-RAY DIFFRACTION99.92
2.36-2.480.2481420.18573409X-RAY DIFFRACTION99.97
2.48-2.640.21931410.18223402X-RAY DIFFRACTION100
2.64-2.840.25111440.18263456X-RAY DIFFRACTION100
2.84-3.120.19831430.18093445X-RAY DIFFRACTION99.94
3.12-3.580.19141430.16663466X-RAY DIFFRACTION99.92
3.58-4.510.15651460.14273503X-RAY DIFFRACTION100
4.51-60.680.17921510.16623630X-RAY DIFFRACTION99.68
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.727062890804-0.2430106310320.1610032571292.32052769311-0.1340768296441.34065028410.0393574387616-0.0465121854954-0.02477847265140.077160079597-0.006038766223890.0531590603122-0.0917115815082-0.0654546001314-0.02668908485640.266748780064-0.007252971120730.03563227654970.314459302315-0.02443111430.245411341193-16.75068961897.2531427465519.4718646508
23.79101646831.03218377186-0.2052335407222.550650428380.4234142241960.852591914863-0.20730331958-0.107016024608-0.5030085294680.08150594798330.0873865372538-0.2068961093090.2438729434810.03618882290130.1161398508890.5122612046220.03362908458190.03626607165680.3103280624660.04424795536530.3469691658197.19026480952-9.581126471355.5195303561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 334 )
2X-RAY DIFFRACTION2chain 'A' and (resid 335 through 514 )

+
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