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- PDB-5esd: Crystal Structure of M. tuberculosis MenD bound to ThDP and Mn2+ -

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Basic information

Entry
Database: PDB / ID: 5esd
TitleCrystal Structure of M. tuberculosis MenD bound to ThDP and Mn2+
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
KeywordsHYDROLASE / 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 (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THIAMINE DIPHOSPHATE / 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: 2.25 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 16, 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: Other
Revision 1.3Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _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 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_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_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _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 / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)242,19712
Polymers240,2764
Non-polymers1,9218
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25460 Å2
ΔGint-124 kcal/mol
Surface area69770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.625, 138.657, 165.386
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 60068.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Protein was purified with an N-terminal his-tag that is not visible in the crystal structure. The numbering of the PDB file matches the numbering of the sequence from the biological start ...Details: Protein was purified with an N-terminal his-tag that is not visible in the crystal structure. The numbering of the PDB file matches the numbering of the sequence from the biological start residue (e.g. M 1 in sequence = M 1 in PDB file).
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
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8% PEG 6000, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.25→19.811 Å / Num. obs: 107885 / % possible obs: 99.8 % / Redundancy: 43.1 % / Biso Wilson estimate: 37.48 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.43 / Rpim(I) all: 0.066 / Net I/σ(I): 14.7 / Num. measured all: 4650184 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.25-2.2937.46.411.119726752700.6151.054100
12.32-19.8138.10.04583.82182057310.00776.8

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata scaling
REFMACrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→19.811 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 5392 5.04 %
Rwork0.2105 101668 -
obs0.2117 107060 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.38 Å2 / Biso mean: 38.4747 Å2 / Biso min: 20.11 Å2
Refinement stepCycle: final / Resolution: 2.25→19.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15813 0 108 481 16402
Biso mean--41.83 32.65 -
Num. residues----2152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516294
X-RAY DIFFRACTIONf_angle_d0.80222330
X-RAY DIFFRACTIONf_chiral_restr0.0472634
X-RAY DIFFRACTIONf_plane_restr0.0062969
X-RAY DIFFRACTIONf_dihedral_angle_d18.759850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.27550.49161510.49792689284080
2.2755-2.30230.33461780.327633633541100
2.3023-2.33030.29851820.313933543536100
2.3303-2.35980.33011720.305933733545100
2.3598-2.39080.3281860.294433803566100
2.3908-2.42350.34451620.29533813543100
2.4235-2.4580.30811720.291434103582100
2.458-2.49460.31381510.299433783529100
2.4946-2.53350.3241750.276134013576100
2.5335-2.5750.29421910.271533953586100
2.575-2.61930.29731680.264233663534100
2.6193-2.66680.32221950.274333943589100
2.6668-2.7180.33082050.27233383543100
2.718-2.77330.28011540.246234173571100
2.7733-2.83340.26491980.248233983596100
2.8334-2.89920.27781900.249333763566100
2.8992-2.97140.26081650.240833973562100
2.9714-3.05150.26341730.234934203593100
3.0515-3.14090.24571890.226933913580100
3.1409-3.24190.23591850.225933933578100
3.2419-3.35720.24491840.209833993583100
3.3572-3.4910.24671740.207634423616100
3.491-3.64890.21712050.191634013606100
3.6489-3.840.2131710.184434293600100
3.84-4.07860.211690.177734543623100
4.0786-4.39040.18991740.158534433617100
4.3904-4.82640.18331720.152234803652100
4.8264-5.51160.16981930.161334793672100
5.5116-6.8950.19392000.182335013701100
6.895-19.8120.17552080.149336263834100

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