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- PDB-9dsn: D306A Mutant of M.tuberculosis MenD (SEPHCHC Synthase) -

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Basic information

Entry
Database: PDB / ID: 9dsn
TitleD306A Mutant of M.tuberculosis MenD (SEPHCHC Synthase)
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsBIOSYNTHETIC PROTEIN / Mycobaterium tuberculosis / menaquinone biosynthesis / MenD / SEPHCHC synthase / allosteric regulator / DHNA / cooperativity / allostery 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 / FORMIC 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: 2.3 Å
AuthorsJohnston, J.M. / Ho, N.A.T. / Given, F.M. / Allison, T.A. / 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
DepositionSep 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)241,76518
Polymers240,1004
Non-polymers1,66514
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, We have variously studied these enzymes by gel filtration, mass spectrometry, mass photometry, AUC and SAXS. We know that these enzymes are predominantely tetramers in ...Evidence: gel filtration, We have variously studied these enzymes by gel filtration, mass spectrometry, mass photometry, AUC and SAXS. We know that these enzymes are predominantely tetramers in solution and consistently tetramers in crystallographic structures.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21920 Å2
ΔGint-105 kcal/mol
Surface area70970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.217, 139.257, 181.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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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: D306A
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 6 types, 475 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 8% PEG 4k, 16% glycerol, 0.02 M each carboxylic acid, 0.1 MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953644 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953644 Å / Relative weight: 1
ReflectionResolution: 2.3→48.75 Å / Num. obs: 114176 / % possible obs: 99.8 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.031 / Rrim(I) all: 0.113 / Χ2: 0.99 / Net I/σ(I): 15.7 / Num. measured all: 1544924
Reflection shellResolution: 2.3→2.34 Å / % possible obs: 95.5 % / Redundancy: 12.6 % / Rmerge(I) obs: 1.59 / Num. measured all: 66776 / Num. unique obs: 5318 / CC1/2: 0.633 / Rpim(I) all: 0.454 / Rrim(I) all: 1.656 / Χ2: 0.98 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.75 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 5791 5.08 %
Rwork0.1918 --
obs0.1937 114042 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15572 0 106 461 16139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416112
X-RAY DIFFRACTIONf_angle_d0.64222097
X-RAY DIFFRACTIONf_dihedral_angle_d6.4142351
X-RAY DIFFRACTIONf_chiral_restr0.0442611
X-RAY DIFFRACTIONf_plane_restr0.0072945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.3191920.29153270X-RAY DIFFRACTION93
2.33-2.350.332170.26923553X-RAY DIFFRACTION100
2.35-2.380.27331880.25923576X-RAY DIFFRACTION100
2.38-2.410.29031940.24783598X-RAY DIFFRACTION100
2.41-2.440.2782050.243529X-RAY DIFFRACTION100
2.44-2.480.2861820.24463618X-RAY DIFFRACTION100
2.48-2.510.29992000.24453553X-RAY DIFFRACTION100
2.51-2.550.36921790.2583588X-RAY DIFFRACTION100
2.55-2.590.34631790.26263614X-RAY DIFFRACTION100
2.59-2.630.30311820.23833601X-RAY DIFFRACTION100
2.63-2.680.28541840.23113598X-RAY DIFFRACTION100
2.68-2.730.29141800.22523597X-RAY DIFFRACTION100
2.73-2.780.26032040.21083588X-RAY DIFFRACTION100
2.78-2.840.27221990.21973564X-RAY DIFFRACTION100
2.84-2.90.2872000.21213615X-RAY DIFFRACTION100
2.9-2.970.26891970.21983589X-RAY DIFFRACTION100
2.97-3.040.27692050.22433570X-RAY DIFFRACTION100
3.04-3.120.27631910.23263611X-RAY DIFFRACTION100
3.12-3.210.29881810.21893615X-RAY DIFFRACTION100
3.21-3.320.27272010.21513623X-RAY DIFFRACTION100
3.32-3.440.23641930.20143603X-RAY DIFFRACTION100
3.44-3.570.22561800.19433651X-RAY DIFFRACTION100
3.57-3.740.23911850.19363634X-RAY DIFFRACTION100
3.74-3.930.20971930.18573630X-RAY DIFFRACTION100
3.93-4.180.22871970.17123652X-RAY DIFFRACTION100
4.18-4.50.1842100.1573618X-RAY DIFFRACTION100
4.5-4.950.16011910.15343675X-RAY DIFFRACTION100
4.95-5.670.20141890.17033706X-RAY DIFFRACTION100
5.67-7.140.21871950.17293729X-RAY DIFFRACTION100
7.14-48.750.15451980.15383883X-RAY DIFFRACTION100

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