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- PDB-5ej6: EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2min the... -

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Basic information

Entry
Database: PDB / ID: 5ej6
TitleEcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 2min then soaked with isochorismate for 2 min
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / Post-decarboxylation intermediate
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 / protein homodimerization activity
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 (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold ...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 (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Chem-TD6 / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.243 Å
AuthorsSong, H.G. / Dong, C. / Chen, Y.Z. / Sun, Y.R. / Guo, Z.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis
Authors: Song, H.G. / Dong, C. / Qin, M.M. / Chen, Y.Z. / Sun, Y.R. / Liu, J.J. / Chan, W. / Guo, Z.H.
History
DepositionNov 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
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
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)496,12924
Polymers491,4708
Non-polymers4,65916
Water33,3101849
1
A: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
B: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,0326
Polymers122,8682
Non-polymers1,1654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-51 kcal/mol
Surface area38340 Å2
MethodPISA
2
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)124,0326
Polymers122,8682
Non-polymers1,1654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-51 kcal/mol
Surface area38210 Å2
MethodPISA
3
E: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
F: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,0326
Polymers122,8682
Non-polymers1,1654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-50 kcal/mol
Surface area38210 Å2
MethodPISA
4
G: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
H: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,0326
Polymers122,8682
Non-polymers1,1654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-50 kcal/mol
Surface area38130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.480, 90.510, 171.640
Angle α, β, γ (deg.)83.02, 75.85, 64.33
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 61433.781 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 substr. MG1655 / Gene: menD, b2264, JW5374 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase
#2: Chemical
ChemComp-TD6 / (4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic acid


Mass: 527.403 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H25N4O10P2S
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1849 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.16 M magnesium formate, 1% tascimate pH 7.0, 0.02 M HEPES pH 7.0, 14% PEG 3350 and 2% PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.24→34.89 Å / Num. obs: 213686 / % possible obs: 93.7 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.7
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.9 / % possible all: 82.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.243→34.888 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2.07 / Phase error: 22.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 10848 5.08 %
Rwork0.1935 --
obs0.196 213650 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.243→34.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34508 0 272 1849 36629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00835644
X-RAY DIFFRACTIONf_angle_d1.15648681
X-RAY DIFFRACTIONf_dihedral_angle_d13.52912839
X-RAY DIFFRACTIONf_chiral_restr0.0495392
X-RAY DIFFRACTIONf_plane_restr0.0066333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.243-2.26850.2963290.21695797X-RAY DIFFRACTION80
2.2685-2.29520.27083280.20566293X-RAY DIFFRACTION87
2.2952-2.32320.29513580.2086321X-RAY DIFFRACTION88
2.3232-2.35260.28893640.20566363X-RAY DIFFRACTION89
2.3526-2.38350.28553450.19386437X-RAY DIFFRACTION89
2.3835-2.41610.27513390.19756503X-RAY DIFFRACTION90
2.4161-2.45070.27523500.2066560X-RAY DIFFRACTION90
2.4507-2.48720.28653430.20776561X-RAY DIFFRACTION92
2.4872-2.52610.26713400.19666593X-RAY DIFFRACTION91
2.5261-2.56750.25433810.20626635X-RAY DIFFRACTION93
2.5675-2.61170.27593350.20616758X-RAY DIFFRACTION93
2.6117-2.65920.26993130.20226803X-RAY DIFFRACTION93
2.6592-2.71030.25013340.2056773X-RAY DIFFRACTION95
2.7103-2.76560.27193210.21226852X-RAY DIFFRACTION94
2.7656-2.82580.27973870.21126917X-RAY DIFFRACTION95
2.8258-2.89150.27173500.20576843X-RAY DIFFRACTION96
2.8915-2.96370.25984000.2086840X-RAY DIFFRACTION96
2.9637-3.04380.25973590.21056918X-RAY DIFFRACTION96
3.0438-3.13330.26133460.2056974X-RAY DIFFRACTION96
3.1333-3.23440.25023330.19627007X-RAY DIFFRACTION96
3.2344-3.34990.23033720.20136933X-RAY DIFFRACTION96
3.3499-3.48390.2363810.19856946X-RAY DIFFRACTION97
3.4839-3.64230.22773850.18986958X-RAY DIFFRACTION97
3.6423-3.83410.20513830.18647003X-RAY DIFFRACTION97
3.8341-4.0740.21723640.18386995X-RAY DIFFRACTION97
4.074-4.3880.19273670.1717060X-RAY DIFFRACTION98
4.388-4.82860.19664280.16796993X-RAY DIFFRACTION98
4.8286-5.52490.21643670.17287050X-RAY DIFFRACTION98
5.5249-6.95170.22484000.18157106X-RAY DIFFRACTION98
6.9517-34.89180.20014460.16967010X-RAY DIFFRACTION98

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