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- PDB-5esu: Crystal Structure of M. tuberculosis MenD bound to Mg2+ and Coval... -

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Basic information

Entry
Database: PDB / ID: 5esu
TitleCrystal Structure of M. tuberculosis MenD bound to Mg2+ and Covalent Intermediate II (a ThDP + de-carboxylated 2-oxoglutarate + Isochorismate adduct)
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsTRANSFERASE / menaquinone biosynthesis / MenD / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase / thiamin-diphosphate dependent enzyme / pyruvate oxidase family
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
BETA-MERCAPTOETHANOL / FORMIC ACID / Chem-TOI / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJohnston, J.M. / Jirgis, E.N.M. / Bashiri, G. / Bulloch, E.M.M. / Baker, E.N.
CitationJournal: Structure / Year: 2016
Title: Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms.
Authors: Jirgis, E.N. / Bashiri, G. / Bulloch, E.M. / Johnston, J.M. / Baker, E.N.
History
DepositionNov 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 20, 2016Group: Database references
Revision 1.3Nov 22, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,10413
Polymers240,2764
Non-polymers1,8289
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22350 Å2
ΔGint-87 kcal/mol
Surface area71030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.450, 139.825, 183.322
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 ABCD

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


Mass: 60068.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This protein contains an N-terminal His-tag that is not observed in the crystal structure. The protein sequence in the PDB file is numbered to match that of the biological sequence (and does ...Details: This protein contains an N-terminal His-tag that is not observed in the crystal structure. The protein sequence in the PDB file is numbered to match that of the biological sequence (and does not number the unseen tag sequence in the numbering). In 2/4 chains the Cys at position 26 has been modified by b-mercaptoethanol in the buffer component
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: menD, Rv0555 / Production host: Mycobacterium smegmatis (bacteria)
References: UniProt: P9WK11, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

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Non-polymers , 5 types, 609 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-TOI / (1~{R},2~{S},5~{S},6~{S})-2-[(1~{S})-1-[3-[(4-azanylidene-2-methyl-1~{H}-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl (phosphonooxy)phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-1,4-bis(oxidanyl)-4-oxidanylidene-butyl]-6-oxidanyl-5-(3-oxid anyl-3-oxidanylidene-prop-1-en-2-yl)oxy-cyclohex-3-ene-1-carboxylic acid / ThDP, decarboxylated 2-oxoglutarate and isochorismate adduct, covalent intermediate II / Thiamine pyrophosphate


Mass: 753.586 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H35N4O16P2S
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 4K, 20% Glycerol, 0.02M CA, pH 7.5 (MORPHEUS G7) [CA=carboxylic acid mix, buffer=MOPS/HEPES-Na]

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→19.853 Å / Num. obs: 130933 / % possible obs: 98.9 % / Redundancy: 15 % / Biso Wilson estimate: 39.57 Å2 / Rmerge(I) obs: 0.176 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 15.3 % / Rmerge(I) obs: 2.461 / Mean I/σ(I) obs: 1.3 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.8data scaling
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.85 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 6634 5.09 %
Rwork0.194 --
obs0.196 130884 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15786 0 115 600 16501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316314
X-RAY DIFFRACTIONf_angle_d0.7422373
X-RAY DIFFRACTIONf_dihedral_angle_d12.1665950
X-RAY DIFFRACTIONf_chiral_restr0.0272650
X-RAY DIFFRACTIONf_plane_restr0.0042980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.38734010.34787968X-RAY DIFFRACTION98
2.225-2.25110.36534470.33697878X-RAY DIFFRACTION98
2.2511-2.27850.36834010.33277973X-RAY DIFFRACTION99
2.2785-2.30730.34473900.31337998X-RAY DIFFRACTION98
2.3073-2.33760.32653730.30437938X-RAY DIFFRACTION99
2.3376-2.36960.33794190.29238042X-RAY DIFFRACTION98
2.3696-2.40340.33654200.28997905X-RAY DIFFRACTION98
2.4034-2.43920.32664520.27387959X-RAY DIFFRACTION99
2.4392-2.47730.30454190.27167914X-RAY DIFFRACTION98
2.4773-2.51780.29774610.25617923X-RAY DIFFRACTION99
2.5178-2.56110.2954180.25077970X-RAY DIFFRACTION99
2.5611-2.60760.30944260.24697951X-RAY DIFFRACTION98
2.6076-2.65760.27384560.23797971X-RAY DIFFRACTION99
2.6576-2.71180.30744510.23457990X-RAY DIFFRACTION99
2.7118-2.77060.28493890.22197982X-RAY DIFFRACTION99
2.7706-2.83480.28274360.22247989X-RAY DIFFRACTION99
2.8348-2.90550.31273930.22968025X-RAY DIFFRACTION99
2.9055-2.98380.27434590.2177991X-RAY DIFFRACTION99
2.9838-3.07130.25844080.2158058X-RAY DIFFRACTION99
3.0713-3.17010.25194590.21097920X-RAY DIFFRACTION99
3.1701-3.28290.25794560.20027967X-RAY DIFFRACTION99
3.2829-3.41370.28044100.19868080X-RAY DIFFRACTION99
3.4137-3.56820.23974620.18417972X-RAY DIFFRACTION99
3.5682-3.75520.20824440.17058056X-RAY DIFFRACTION99
3.7552-3.98870.20124120.16588048X-RAY DIFFRACTION100
3.9887-4.29370.21474020.15848042X-RAY DIFFRACTION100
4.2937-4.72060.16084310.13718074X-RAY DIFFRACTION100
4.7206-5.39170.18313990.14638116X-RAY DIFFRACTION100
5.3917-6.74830.19474890.15597999X-RAY DIFFRACTION100
6.7483-19.85410.14234690.12618010X-RAY DIFFRACTION100

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