[English] 日本語
Yorodumi
- PDB-7ol1: The X-ray structure of L-threonine dehydrogenase from the common ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ol1
TitleThe X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / apoenzyme.
Function / homologyL-threonine 3-dehydrogenase / : / L-threonine 3-dehydrogenase activity / threonine catabolic process / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / L-threonine 3-dehydrogenase
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGuo, J. / Cooper, J.B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: The X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.
Authors: Adjogatse, E. / Bennett, J. / Guo, J. / Erskine, P.T. / Wood, S.P. / Wren, B.W. / Cooper, J.B.
History
DepositionMay 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)76,4172
Polymers76,4172
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Likely to be dimeric based on gel-filtration and crystallographic studies of related short-chain TDHs and PISA analysis of buried surface area and contacts (Krissinel, E. & Henrick, K. ...Evidence: Likely to be dimeric based on gel-filtration and crystallographic studies of related short-chain TDHs and PISA analysis of buried surface area and contacts (Krissinel, E. & Henrick, K. (2007). J. Molec. Biol. 372, 774-797).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-14 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.870, 180.870, 88.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein L-threonine 3-dehydrogenase / L-threonine dehydrogenase / UDP-glucose 4-epimerase / Uncharacterized epimerase/dehydratase SAV0553


Mass: 38208.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal sequence MGHHHHHHHHHHSSGHIEGRH originates from the expression tag.
Source: (gene. exp.) Clostridioides difficile (bacteria)
Gene: cdgr_08060, NCTC13307_02322, SAMEA1402406_00083, SAMEA3375037_00176
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A346VYB9, L-threonine 3-dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 5.8 Å3/Da / Density % sol: 78.9 % / Description: Multifaceted.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5 microlitres of enzyme at a concentration of 5 mg/ml and 5 microlitres of 0.2 M lithium sulphate, 0.1 M Tris-HCl pH 8.5, 30 % v/v PEG 4000 (Molecular Dimensions Limited Structure Screen I, condition 35).
Temp details: Ambient temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.56→63.28 Å / Num. obs: 53475 / % possible obs: 99.5 % / Redundancy: 9.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.04 / Rrim(I) all: 0.125 / Rsym value: 0.118 / Net I/av σ(I): 4.2 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.56-2.78.31.7780.477580.5260.6461.8971.77899.4
2.7-2.8691.1680.773220.4071.2391.16899.6
2.86-3.069.40.7121.169090.2420.7530.71299.8
3.06-3.38.50.3342.364050.1210.3560.33499.2
3.3-3.6210.10.1784.259260.0580.1870.17899.6
3.62-4.0510.30.099753830.0320.1040.09999.6
4.05-4.679.70.0689.547710.0230.0720.06899.5
4.67-5.729.50.0618.840310.0210.0650.06199.2
5.72-8.110.20.0666.831710.0210.0690.06699.8
8.1-63.1979.50.0627.917990.0210.0650.06299.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5lc1

5lc1


Resolution: 2.6→63.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.429 / SU ML: 0.198 / SU R Cruickshank DPI: 0.234 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.234 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 2500 5 %RANDOM
Rwork0.2004 ---
obs0.2024 47443 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 205.04 Å2 / Biso mean: 75.367 Å2 / Biso min: 27.12 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å2-1.47 Å2-0 Å2
2---2.95 Å20 Å2
3---9.56 Å2
Refinement stepCycle: final / Resolution: 2.6→63.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 0 112 5142
Biso mean---66.63 -
Num. residues----638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174875
X-RAY DIFFRACTIONr_angle_refined_deg1.791.6436938
X-RAY DIFFRACTIONr_angle_other_deg1.2971.58311296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6375636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91123.629248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.79715928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0261522
X-RAY DIFFRACTIONr_chiral_restr0.0790.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025746
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021107
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 156 -
Rwork0.367 2989 -
all-3145 -
obs--83.2 %

+
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