[English] 日本語
Yorodumi
- PDB-2gn2: Crystal structure of tetrameric biodegradative threonine deaminas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gn2
TitleCrystal structure of tetrameric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium in complex with CMP at 2.5A resolution (Hexagonal form)
ComponentsThreonine dehydratase catabolic
KeywordsLYASE / TdcB / Biodegradative threonine deaminase / PLP / CMP / Threonine dehydratase / L-threonine metabolism
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / L-threonine catabolic process to propionate / threonine catabolic process / L-serine ammonia-lyase / L-serine ammonia-lyase activity / L-serine catabolic process / isoleucine biosynthetic process / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Threonine dehydratase, catabolic / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / L-threonine dehydratase catabolic TdcB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSimanshu, D.K. / Savithri, H.S. / Murthy, M.R.N.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation.
Authors: Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray crystallographic analysis of biodegradative threonine deaminase (TdcB) from Salmonella typhimurium
Authors: Simanshu, D.K. / Chittori, S. / Savithri, H.S. / Murthy, M.R.
History
DepositionApr 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: 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 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / 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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Threonine dehydratase catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2333
Polymers36,8871
Non-polymers3462
Water1,11762
1
A: Threonine dehydratase catabolic
hetero molecules

A: Threonine dehydratase catabolic
hetero molecules

A: Threonine dehydratase catabolic
hetero molecules

A: Threonine dehydratase catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,93312
Polymers147,5484
Non-polymers1,3858
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation10_445-y-1,-x-1,-z1
Unit cell
Length a, b, c (Å)161.145, 161.145, 68.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-401-

NA

21A-462-

HOH

31A-463-

HOH

DetailsThe monomeric molecule is centered at the point of 222 symmetry. The biological assembly is a teramer generated from the monomer in the asymmetric unit by the operations: -Y,-X,-Z ; -X, -Y, Z; Y, X, -Z.

-
Components

#1: Protein Threonine dehydratase catabolic / Threonine deaminase


Mass: 36887.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: IFO 12529 / Gene: tdcB / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P11954, threonine ammonia-lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Citrate, 25% PEG4000, 10% Hexanediol , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.93 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 20, 2006 / Details: Osmic mirror
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 18675 / Num. obs: 18675 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 39.32 % / Biso Wilson estimate: 66 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 53.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 7.56 / Num. unique all: 1820 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB CODE 1GN0)

1gn0


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.455 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 951 5.1 %RANDOM
Rwork0.1967 ---
obs0.19823 17629 99.63 %-
all-17629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.336 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å20 Å2
2---1.06 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 22 62 2516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222484
X-RAY DIFFRACTIONr_bond_other_d0.0010.022325
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9923362
X-RAY DIFFRACTIONr_angle_other_deg0.71735411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10524.83993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16515436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2231514
X-RAY DIFFRACTIONr_chiral_restr0.0570.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
X-RAY DIFFRACTIONr_nbd_refined0.1980.2511
X-RAY DIFFRACTIONr_nbd_other0.1630.22317
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21272
X-RAY DIFFRACTIONr_nbtor_other0.080.21465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.280
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1260.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0640.21
X-RAY DIFFRACTIONr_mcbond_it0.2721.51606
X-RAY DIFFRACTIONr_mcbond_other0.051.5677
X-RAY DIFFRACTIONr_mcangle_it0.5322581
X-RAY DIFFRACTIONr_scbond_it0.8833891
X-RAY DIFFRACTIONr_scangle_it1.5094.5781
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 66 -
Rwork0.238 1254 -
obs-1254 97.92 %
Refinement TLS params.Method: refined / Origin x: -17.6753 Å / Origin y: -70.1772 Å / Origin z: -20.1978 Å
111213212223313233
T-0.1911 Å20.1489 Å2-0.0612 Å2--0.0229 Å2-0.0999 Å2---0.128 Å2
L2.9715 °2-0.0306 °2-0.2122 °2-2.0612 °20.1766 °2--2.0035 °2
S-0.0438 Å °-0.5148 Å °0.3265 Å °0.2732 Å °0.2005 Å °-0.3553 Å °-0.1522 Å °0.1058 Å °-0.1567 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://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