[English] 日本語
Yorodumi
- PDB-1tdj: THREONINE DEAMINASE (BIOSYNTHETIC) FROM E. COLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tdj
TitleTHREONINE DEAMINASE (BIOSYNTHETIC) FROM E. COLI
ComponentsBIOSYNTHETIC THREONINE DEAMINASE
KeywordsALLOSTERY / COOPERATIVE / TETRAMER / REGULATION / PYRIDOXAL PHOSPHATE / ISOLEUCINE BIOSYNTHESIS
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
Biosynthetic Threonine Deaminase; domain 3 / Biosynthetic Threonine Deaminase; Domain 3 / 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. ...Biosynthetic Threonine Deaminase; domain 3 / Biosynthetic Threonine Deaminase; Domain 3 / 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 / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / L-threonine dehydratase biosynthetic IlvA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.8 Å
AuthorsGallagher, D.T. / Gilliland, G.L. / Xiao, G. / Eisenstein, E.
Citation
Journal: Structure / Year: 1998
Title: Structure and control of pyridoxal phosphate dependent allosteric threonine deaminase.
Authors: Gallagher, D.T. / Gilliland, G.L. / Xiao, G. / Zondlo, J. / Fisher, K.E. / Chinchilla, D. / Eisenstein, E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Polymorphous Crystallization and Diffraction of Threonine Deaminase from Escherichia Coli
Authors: Gallagher, D.T. / Eisenstein, E. / Fisher, K.E. / Zondlo, J. / Chinchilla, D. / Yu, H.D. / Dill, J. / Winborne, E. / Ducote, K. / Xiao, G. / Gilliland, G.L.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
A: BIOSYNTHETIC THREONINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5102
Polymers56,2631
Non-polymers2471
Water59433
1
A: BIOSYNTHETIC THREONINE DEAMINASE
hetero molecules

A: BIOSYNTHETIC THREONINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0204
Polymers112,5262
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)85.100, 90.800, 162.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein BIOSYNTHETIC THREONINE DEAMINASE / THREONINE DEHYDRATASE


Mass: 56263.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SCHIFF BASE LINKAGE BETWEEN LYS 62 AND PLP / Source: (natural) Escherichia coli (E. coli) / Cellular location: CYTOPLASM / References: UniProt: P04968, EC: 4.2.1.16
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 46 % / Description: C-DOMAIN IMAGED BY IMR
Crystal growpH: 8
Details: PROTEIN AT 40 MG/ML WAS MIXED WITH, THEN EQUILIBRATED OVER 11% PEG 4K, 40 MM TRIS 8.0, 60 MM MGCL2, AT RT.
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Gallagher, D.T., (1998) Acta Crystallogr.,Sect.D, 54, 467.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG40001reservoir
240 mMTris1reservoir
370 mM1reservoirMgCl2
40.2 M1reservoirKCl
530 mg/mlprotain1drop
650 mMpotassium phosphate1drop
70.1 mMdithiothreitol1drop
80.1 mMethylene diamine tetraacetic acid1drop

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→16 Å / Num. obs: 13860 / % possible obs: 78 % / Observed criterion σ(I): 0.5 / Redundancy: 2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.088 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 1 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.372 / % possible all: 30

-
Processing

Software
NameVersionClassification
PHASESphasing
TNT5Erefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.8→16 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: THE 61 ATOMS WITH B=100.0 MUST BE CONSIDERED TO BE MARGINALLY ORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.34 1009 7.5 %RANDOM SUBSET
Rwork0.2 ---
all0.21 13542 --
obs0.21 13542 86 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.56 e/Å3
Refinement stepCycle: LAST / Resolution: 2.8→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 15 33 3848
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0238910.8
X-RAY DIFFRACTIONt_angle_deg2.952381.7
X-RAY DIFFRACTIONt_dihedral_angle_d21.423300
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.018941
X-RAY DIFFRACTIONt_gen_planes0.0225783
X-RAY DIFFRACTIONt_it2.1387522
X-RAY DIFFRACTIONt_nbd0.03213517
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg21.40
X-RAY DIFFRACTIONt_planar_d0.0181
X-RAY DIFFRACTIONt_plane_restr0.0223

+
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