[English] 日本語
Yorodumi
- PDB-9dtv: Structure of D141A mutant of M.tuberculosis MenD (SEPHCHC Synthase) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dtv
TitleStructure of D141A mutant of M.tuberculosis MenD (SEPHCHC Synthase)
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsBIOSYNTHETIC PROTEIN / M.tuberculosis / Menaquinone biosynthesis / allostery / DHNA / MenD mutant D141A / SEPHCHC Synthase mutant
Function / homology
Function and homology information


2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / plasma membrane
Similarity search - Function
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
1,4-dihydroxy-2-naphthoic acid / THIAMINE DIPHOSPHATE / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsJohnston, J.M. / Ho, N.A.T. / Given, F.M. / Allison, T.M. / Bulloch, E.M.M. / Jiao, W.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandM1208 New Zealand
CitationJournal: Chembiochem / Year: 2025
Title: Apparent Reversal of Allosteric Response in Mycobacterium tuberculosis MenD Reveals Links to Half-of-Sites Reactivity.
Authors: Ho, N.A.T. / Given, F.M. / Stanborough, T. / Klein, M. / Allison, T.M. / Bulloch, E.M.M. / Jiao, W. / Johnston, J.M.
History
DepositionOct 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
D: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
C: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,83118
Polymers240,1004
Non-polymers1,73114
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, We have variously done gel filtration, AUC, SAXS and mass photometry on these enzymes.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23650 Å2
ΔGint-146 kcal/mol
Surface area72060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.425, 140.443, 184.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ADBC

#1: Protein
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / SEPHCHC synthase / Menaquinone biosynthesis protein MenD


Mass: 60024.930 Da / Num. of mol.: 4 / Mutation: D141A
Source method: isolated from a genetically manipulated source
Details: N-terminal His-tag (0 to -19), start site at start of wild type natural sequence (position 1 in PDB file) and an engineered mutation D141A.
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: menD, Rv0555 / Production host: Mycolicibacterium smegmatis (bacteria)
References: UniProt: P9WK11, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

-
Non-polymers , 7 types, 157 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DNA / 1,4-dihydroxy-2-naphthoic acid / 1,4-dihydroxynaphthalene-2-carboxylic acid


Mass: 204.179 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 6% w/v PEG8K, 12% ethylene glycol, halide mix (NaI, NaBr, NaF) 0.03M each, 0.1 M MOPS/HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.42→49.19 Å / Num. obs: 100844 / % possible obs: 100 % / Redundancy: 27 % / CC1/2: 0.999 / Rmerge(I) obs: 0.269 / Rpim(I) all: 0.053 / Rrim(I) all: 0.275 / Χ2: 1.01 / Net I/σ(I): 12.4 / Num. measured all: 2724267
Reflection shellResolution: 2.42→2.46 Å / % possible obs: 100 % / Redundancy: 27.7 % / Rmerge(I) obs: 5.234 / Num. measured all: 136321 / Num. unique obs: 4917 / CC1/2: 0.302 / Rpim(I) all: 1.007 / Rrim(I) all: 5.331 / Χ2: 0.69 / Net I/σ(I) obs: 0.7

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→44.42 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 5082 5.05 %
Rwork0.1933 --
obs0.1953 100732 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15694 0 105 143 15942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316247
X-RAY DIFFRACTIONf_angle_d0.59922282
X-RAY DIFFRACTIONf_dihedral_angle_d15.6815886
X-RAY DIFFRACTIONf_chiral_restr0.0422629
X-RAY DIFFRACTIONf_plane_restr0.0062969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.450.41152000.35293086X-RAY DIFFRACTION100
2.45-2.480.36621770.35183167X-RAY DIFFRACTION100
2.48-2.510.34371390.32833164X-RAY DIFFRACTION100
2.51-2.540.34351600.28943153X-RAY DIFFRACTION100
2.54-2.570.35511640.2833120X-RAY DIFFRACTION100
2.57-2.610.35541800.27873195X-RAY DIFFRACTION100
2.61-2.640.34661490.27343132X-RAY DIFFRACTION100
2.64-2.680.32291750.27283170X-RAY DIFFRACTION100
2.68-2.730.35671790.26473155X-RAY DIFFRACTION100
2.73-2.770.33371710.27043145X-RAY DIFFRACTION100
2.77-2.820.28821710.25743171X-RAY DIFFRACTION100
2.82-2.870.33511900.26113149X-RAY DIFFRACTION100
2.87-2.920.26791410.26033192X-RAY DIFFRACTION100
2.92-2.980.32271730.26173169X-RAY DIFFRACTION100
2.98-3.050.32471820.26033167X-RAY DIFFRACTION100
3.05-3.120.33621650.25983152X-RAY DIFFRACTION100
3.12-3.20.29421600.23973173X-RAY DIFFRACTION100
3.2-3.280.28641490.23183217X-RAY DIFFRACTION100
3.28-3.380.27211750.2283188X-RAY DIFFRACTION100
3.38-3.490.26751340.22093195X-RAY DIFFRACTION100
3.49-3.610.2211820.20463196X-RAY DIFFRACTION100
3.61-3.760.22921690.17993183X-RAY DIFFRACTION100
3.76-3.930.22421730.16983182X-RAY DIFFRACTION100
3.93-4.140.1971630.1583223X-RAY DIFFRACTION100
4.14-4.40.16531810.14823197X-RAY DIFFRACTION100
4.4-4.740.1841830.14213203X-RAY DIFFRACTION100
4.74-5.210.17151950.15143199X-RAY DIFFRACTION100
5.21-5.960.23081480.17513302X-RAY DIFFRACTION100
5.96-7.510.21561720.17283288X-RAY DIFFRACTION100
7.51-44.420.17341820.14783417X-RAY DIFFRACTION100

+
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