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- PDB-5ej8: EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate fo... -

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Basic information

Entry
Database: PDB / ID: 5ej8
TitleEcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate 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
FORMIC ACID / : / 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: 1.34 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_conn_angle / 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_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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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)501,280120
Polymers491,4708
Non-polymers9,809112
Water102,2535676
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)125,43933
Polymers122,8682
Non-polymers2,57131
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-44 kcal/mol
Surface area36750 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)125,46931
Polymers122,8682
Non-polymers2,60129
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-35 kcal/mol
Surface area36410 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)125,07426
Polymers122,8682
Non-polymers2,20624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-62 kcal/mol
Surface area37070 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)125,29830
Polymers122,8682
Non-polymers2,43128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-58 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.660, 90.760, 169.340
Angle α, β, γ (deg.)83.25, 76.03, 64.32
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / ThDP-dependent emzyme 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 / 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

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Non-polymers , 8 types, 5788 molecules

#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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical...
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5676 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
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: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.34→27.65 Å / Num. obs: 1002427 / % possible obs: 94.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 5
Reflection shellResolution: 1.34→1.39 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.34→27.649 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 15.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1636 50280 5.02 %
Rwork0.1328 --
obs0.1343 1002337 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.34→27.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms34267 0 598 5676 40541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836936
X-RAY DIFFRACTIONf_angle_d1.06550498
X-RAY DIFFRACTIONf_dihedral_angle_d22.47113334
X-RAY DIFFRACTIONf_chiral_restr0.0795553
X-RAY DIFFRACTIONf_plane_restr0.0076620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.35520.241816920.191730980X-RAY DIFFRACTION92
1.3552-1.37120.234916050.178631096X-RAY DIFFRACTION93
1.3712-1.38790.221915900.170431124X-RAY DIFFRACTION93
1.3879-1.40550.218516380.168931142X-RAY DIFFRACTION93
1.4055-1.4240.216316410.161931284X-RAY DIFFRACTION93
1.424-1.44350.209816960.158831236X-RAY DIFFRACTION93
1.4435-1.46410.203216710.154431404X-RAY DIFFRACTION93
1.4641-1.48590.19616870.150131314X-RAY DIFFRACTION94
1.4859-1.50910.189616410.143431467X-RAY DIFFRACTION94
1.5091-1.53390.187117040.139831487X-RAY DIFFRACTION94
1.5339-1.56030.183816370.138331530X-RAY DIFFRACTION94
1.5603-1.58870.181717040.131331503X-RAY DIFFRACTION94
1.5887-1.61930.176616420.127531684X-RAY DIFFRACTION94
1.6193-1.65230.171716540.125831647X-RAY DIFFRACTION94
1.6523-1.68820.169416160.123431794X-RAY DIFFRACTION94
1.6882-1.72750.166717040.126131715X-RAY DIFFRACTION95
1.7275-1.77070.165417330.122131805X-RAY DIFFRACTION95
1.7707-1.81860.162117070.121531782X-RAY DIFFRACTION95
1.8186-1.87210.154116900.119831871X-RAY DIFFRACTION95
1.8721-1.93250.157617180.11832024X-RAY DIFFRACTION95
1.9325-2.00150.157716810.122331885X-RAY DIFFRACTION95
2.0015-2.08160.147217040.117631936X-RAY DIFFRACTION95
2.0816-2.17630.150916820.118431958X-RAY DIFFRACTION95
2.1763-2.2910.143816760.1231906X-RAY DIFFRACTION95
2.291-2.43450.143416770.117531882X-RAY DIFFRACTION95
2.4345-2.62230.145517450.119931657X-RAY DIFFRACTION94
2.6223-2.8860.148716680.126731749X-RAY DIFFRACTION94
2.886-3.3030.14917600.127732840X-RAY DIFFRACTION98
3.303-4.15910.153816250.137933176X-RAY DIFFRACTION98
4.1591-27.65480.174216920.157633179X-RAY DIFFRACTION99

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