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- PDB-9e9b: Crystal structure of L. monocytogenes MenD with Mg2+ and ThDP bound -

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Basic information

Entry
Database: PDB / ID: 9e9b
TitleCrystal structure of L. monocytogenes MenD with Mg2+ and ThDP bound
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / SEPHCHC synthase Decarboxylase ThDP-dependent enzyme
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
Similarity search - Function
Menaquinone biosynthesis protein MenD, middle domain / Middle domain of thiamine pyrophosphate / 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 / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
THIAMINE DIPHOSPHATE / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesListeria monocytogenes 10403S (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsKlein, M. / Given, F.M. / Ho, N.A.T. / Allison, T.M. / Johnston, J.M.
Funding support New Zealand, Germany, 2items
OrganizationGrant numberCountry
Marsden FundM1208 New Zealand
Other governmentGerman Academic Exchange Service/Deutscher Akademischer Austauschdienst (DAAD) Germany
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Structures of Listeria monocytogenes MenD in ThDP-bound and in-crystallo captured intermediate I-bound forms.
Authors: Bailey, M. / Given, F.M. / Ho, N.A.T. / Pearce, F.G. / Allison, T.M. / Johnston, J.M.
History
DepositionNov 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,3793
Polymers64,9301
Non-polymers4502
Water1,18966
1
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules

A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,51612
Polymers259,7184
Non-polymers1,7988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_455-x+y-1,y,-z1
Buried area28140 Å2
ΔGint-200 kcal/mol
Surface area69720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.025, 176.025, 100.144
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3
Components on special symmetry positions
IDModelComponents
11A-719-

HOH

21A-766-

HOH

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Components

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


Mass: 64929.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes 10403S (bacteria)
Gene: menD, LMRG_01292 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H3GD77, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
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: 3.45 Å3/Da / Density % sol: 64.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1M MOPS/HEPES-Na pH7.5, 0.02M 1,6-hexanediol, 0.02M 1-butanol, 0.02M (RS)-1,2-propanediol, 0.02M 2-propanol, 0.02M 1,4-butanediol, 0. ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.1M MOPS/HEPES-Na pH7.5, 0.02M 1,6-hexanediol, 0.02M 1-butanol, 0.02M (RS)-1,2-propanediol, 0.02M 2-propanol, 0.02M 1,4-butanediol, 0.02M 1,3-propanediol, 5 mM MgCl2, 1 mM ThDP, 1 mM TCEP

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.61→47.57 Å / Num. obs: 28314 / % possible obs: 100 % / Redundancy: 54.5 % / Biso Wilson estimate: 52.58 Å2 / CC1/2: 0.994 / Net I/σ(I): 14.6
Reflection shellResolution: 2.61→2.73 Å / Num. unique obs: 3395 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→47.57 Å / SU ML: 0.2513 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.239
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 1410 4.99 %
Rwork0.1991 26868 -
obs0.2009 28278 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.77 Å2
Refinement stepCycle: LAST / Resolution: 2.61→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4535 0 27 66 4628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034665
X-RAY DIFFRACTIONf_angle_d0.52766332
X-RAY DIFFRACTIONf_chiral_restr0.0428708
X-RAY DIFFRACTIONf_plane_restr0.0048814
X-RAY DIFFRACTIONf_dihedral_angle_d16.3561723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.70.3241480.27142630X-RAY DIFFRACTION100
2.7-2.810.31071370.26432626X-RAY DIFFRACTION100
2.81-2.940.26241420.25772647X-RAY DIFFRACTION100
2.94-3.090.28511210.24762652X-RAY DIFFRACTION100
3.09-3.290.27971340.25042659X-RAY DIFFRACTION100
3.29-3.540.28161430.2442661X-RAY DIFFRACTION99.89
3.54-3.90.24291470.19312672X-RAY DIFFRACTION99.86
3.9-4.460.2111470.17622690X-RAY DIFFRACTION99.89
4.46-5.620.19821470.16152735X-RAY DIFFRACTION99.97
5.62-47.570.19061440.16182896X-RAY DIFFRACTION99.84

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