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- PDB-7tin: The Structure of S. aureus MenD -

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Basic information

Entry
Database: PDB / ID: 7tin
TitleThe Structure of S. aureus MenD
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / Menaquinone biosynthesis / MenD / SEPHCHC Synthase
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
Similarity search - Domain/homology
GLYCINE / THIAMINE DIPHOSPHATE / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsJohnston, J.M. / Stanborough, T. / Ho, N.A.T. / Akazong, E.W. / Jiao, W.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandM1208 New Zealand
CitationJournal: Philos.Trans.R.Soc.Lond.B Biol.Sci. / Year: 2023
Title: Allosteric inhibition of Staphylococcus aureus MenD by 1,4-dihydroxy naphthoic acid: a feedback inhibition mechanism of the menaquinone biosynthesis pathway.
Authors: Stanborough, T. / Ho, N.A.T. / Bulloch, E.M.M. / Bashiri, G. / Dawes, S.S. / Akazong, E.W. / Titterington, J. / Allison, T.M. / Jiao, W. / Johnston, J.M.
History
DepositionJan 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)255,67524
Polymers253,1604
Non-polymers2,51420
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27230 Å2
ΔGint-253 kcal/mol
Surface area69580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.445, 166.489, 168.035
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 63290.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: menD, BSG37_05155, E5491_05050, FAF32_004775, G6X35_16435, G6X37_01395, G6Y24_06155, GO810_06740, SAMEA103891454_01695
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A390C306, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

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Non-polymers , 6 types, 268 molecules

#2: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Morph H12. 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 0.02 M of each amino acid 0.1 M bicine/Trizma base pH 8.5

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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: Jun 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.35→47.85 Å / Num. obs: 95884 / % possible obs: 100 % / Redundancy: 26.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.284 / Rpim(I) all: 0.056 / Rrim(I) all: 0.289 / Net I/σ(I): 11.5 / Num. measured all: 2563352
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.3926.93.9312742247310.3460.7644.006199.8
12.87-47.8520.30.056137806790.9990.0120.05753.698.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
REFMAC1.0.2refinement
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X7J

2x7j


Resolution: 2.35→46.47 Å / SU ML: 0.3409 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.9301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2355 4853 5.07 %
Rwork0.1874 90899 -
obs0.1898 95752 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.37 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17679 0 148 248 18075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002918221
X-RAY DIFFRACTIONf_angle_d0.565924725
X-RAY DIFFRACTIONf_chiral_restr0.04492773
X-RAY DIFFRACTIONf_plane_restr0.00423178
X-RAY DIFFRACTIONf_dihedral_angle_d5.94872429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.380.33461530.30132987X-RAY DIFFRACTION98.46
2.38-2.40.34981620.29392984X-RAY DIFFRACTION99.97
2.4-2.430.30591520.32988X-RAY DIFFRACTION100
2.43-2.460.35381620.28353020X-RAY DIFFRACTION100
2.46-2.50.3671480.28622972X-RAY DIFFRACTION100
2.5-2.530.33951460.27683008X-RAY DIFFRACTION100
2.53-2.570.33681650.27462990X-RAY DIFFRACTION100
2.57-2.610.33681890.27052987X-RAY DIFFRACTION100
2.61-2.650.30551600.26792990X-RAY DIFFRACTION100
2.65-2.690.33661520.26583021X-RAY DIFFRACTION100
2.69-2.740.36281540.25923015X-RAY DIFFRACTION100
2.74-2.790.31211700.25293000X-RAY DIFFRACTION100
2.79-2.840.27641920.23822965X-RAY DIFFRACTION100
2.84-2.90.27981540.23233021X-RAY DIFFRACTION100
2.9-2.960.30051380.22783022X-RAY DIFFRACTION100
2.96-3.030.2711460.21663041X-RAY DIFFRACTION100
3.03-3.110.24711560.21573000X-RAY DIFFRACTION100
3.11-3.190.27661720.22163006X-RAY DIFFRACTION100
3.19-3.280.28321780.22653022X-RAY DIFFRACTION100
3.28-3.390.22581750.19353021X-RAY DIFFRACTION100
3.39-3.510.24031670.17883005X-RAY DIFFRACTION100
3.51-3.650.20271820.16813020X-RAY DIFFRACTION100
3.65-3.820.22641550.16323040X-RAY DIFFRACTION100
3.82-4.020.221420.16213065X-RAY DIFFRACTION100
4.02-4.270.19991560.15713075X-RAY DIFFRACTION100
4.27-4.60.21041650.14973040X-RAY DIFFRACTION100
4.6-5.060.20111600.14973100X-RAY DIFFRACTION100
5.06-5.790.22381460.163121X-RAY DIFFRACTION100
5.79-7.290.20311720.17443117X-RAY DIFFRACTION99.97
7.3-46.470.1631840.14393256X-RAY DIFFRACTION99.71

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