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- PDB-6o0j: M.tb MenD with ThDP and Inhibitor bound -

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Basic information

Entry
Database: PDB / ID: 6o0j
TitleM.tb MenD with ThDP and Inhibitor bound
Components2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase
Keywordstransferase/transferase inhibitor / menaquinone biosynthesis / ThDP dependent / decarboxylation / C-C bond ligation / Inhibitor complex / SEPHCHC synthase / transferase-transferase inhibitor complex
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
ACETATE ION / 1,4-dihydroxy-2-naphthoic acid / FORMIC ACID / 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: 2.35 Å
AuthorsJohnston, J.M. / Bashiri, G. / Bulloch, E.M.M. / Jirgis, E.M.N. / Nigon, L.V. / Chuang, H. / Ho, N.A.T. / Baker, E.N.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New Zealand New Zealand
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogenMycobacterium tuberculosis.
Authors: Bashiri, G. / Nigon, L.V. / Jirgis, E.N.M. / Ho, N.A.T. / Stanborough, T. / Dawes, S.S. / Baker, E.N. / Bulloch, E.M.M. / Johnston, J.M.
History
DepositionFeb 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Aug 4, 2021Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / 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_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _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_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.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 2.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
D: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,49120
Polymers240,2764
Non-polymers2,21516
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24470 Å2
ΔGint-85 kcal/mol
Surface area66880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.553, 143.673, 176.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ADBC

#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
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: menD, Rv0555
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: P9WK11, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase

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Non-polymers , 7 types, 487 molecules

#2: Chemical
ChemComp-DNA / 1,4-dihydroxy-2-naphthoic acid / 1,4-dihydroxynaphthalene-2-carboxylic acid


Mass: 204.179 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H8O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: MORPH condition, HEPES/MOPS, PEG 4K, CA mix, glycerol,

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→48.81 Å / Num. obs: 107806 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.075 / Rrim(I) all: 0.29 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.39154.34952800.3561.1584.501100
12.87-48.8111.70.0337570.9990.010.03498.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.15data scaling
PHENIX1.14_3260refinement
REFMACrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ESU

5esu


Resolution: 2.35→48.789 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.39
RfactorNum. reflection% reflection
Rfree0.2505 5372 4.99 %
Rwork0.2055 --
obs0.2077 107622 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.6 Å2 / Biso mean: 57.3125 Å2 / Biso min: 25.65 Å2
Refinement stepCycle: final / Resolution: 2.35→48.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15265 0 147 471 15883
Biso mean--46 48.11 -
Num. residues----2119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.37670.40371930.360933523545100
2.3767-2.40470.36071760.334633473523100
2.4047-2.4340.36181800.329233543534100
2.434-2.46480.37561880.326133903578100
2.4648-2.49720.37821780.333733643542100
2.4972-2.53140.36831730.314833663539100
2.5314-2.56760.36511640.293833823546100
2.5676-2.60590.33991850.285634093594100
2.6059-2.64660.32491900.283133463536100
2.6466-2.690.36541600.278533623522100
2.69-2.73640.32451920.26834003592100
2.7364-2.78620.35321480.263233903538100
2.7862-2.83980.31051750.260434353610100
2.8398-2.89770.31791810.259133493530100
2.8977-2.96070.3191820.253433943576100
2.9607-3.02960.31821760.252833843560100
3.0296-3.10530.31731820.248333733555100
3.1053-3.18930.29521770.242234273604100
3.1893-3.28310.29021900.231933833573100
3.2831-3.3890.26231930.213334093602100
3.389-3.51010.23491790.199133993578100
3.5101-3.65060.22951920.191733663558100
3.6506-3.81670.22621690.186234603629100
3.8167-4.01790.22171940.179433993593100
4.0179-4.26950.22791740.166934263600100
4.2695-4.59890.18791550.146434823637100
4.5989-5.06120.18581740.149934613635100
5.0612-5.79260.1991850.168234653650100
5.7926-7.29420.19991740.168135403714100
7.2942-48.79960.1771930.15573636382999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9380.25010.44211.45510.27661.1390.033-0.1306-0.21710.1687-0.08550.09830.2238-0.12150.05370.3483-0.05330.08030.35380.02070.3757-6.06-13.977-4.19
22.4153-2.1938-1.48013.95912.71112.0088-0.1346-0.25730.01570.8471-0.0240.13630.2579-0.08030.1680.5463-0.03690.0870.4576-0.04220.309-5.04611.55223.721
32.6395-2.4816-2.25023.1522.96952.72820.1139-0.220.41370.2234-0.0263-0.0424-0.0787-0.0433-0.09690.4797-0.0110.08720.4473-0.05640.4255-5.13517.53322.785
42.4482-0.1645-0.17892.12141.37123.1272-0.089-0.4030.16560.4489-0.12350.39690.1579-0.45880.18860.4-0.050.1930.6294-0.11840.5175-25.1312.58711.928
50.43020.27560.71951.21391.31381.8971-0.0565-0.44690.49070.218-0.36160.4807-0.1087-0.68570.49280.47050.06850.07710.8468-0.26570.9781-33.5459.2917.565
61.18520.7074-0.31391.5011-0.15011.7903-0.06090.0809-0.1918-0.08960.0005-0.19190.10560.23060.04980.30220.02280.07380.32910.01640.378320.242-5.7-24.387
72.6611-0.08040.98363.09440.37133.00680.01040.116-0.3514-0.3289-0.0113-0.13140.27950.05050.02410.2965-0.01160.12690.295-0.01440.328110.109-11.58-30.228
81.6815-0.15150.46752.2398-0.86441.0211-0.02440.17890.1384-0.48680.017-0.1451-0.23450.07630.0040.6053-0.05220.10310.41320.04180.339822.23822.358-38.141
95.36043.3321-5.37165.1996-3.33595.35681.4941.01651.00660.68930.2817-0.5559-0.3374-0.6911-1.69110.7756-0.0018-0.05720.73840.06040.749337.00923.5-13.589
100.6265-0.5116-0.02414.6898-1.24970.672-0.0242-0.06140.0113-0.211-0.1906-0.665-0.10980.31910.23020.4749-0.1130.10640.60480.06340.733141.93421.147-30.675
112.4792-0.6621-0.00821.36421.13372.62470.0152-0.11270.5825-0.10410.0323-0.2432-0.57580.3419-0.03860.4072-0.09330.00060.4148-0.00080.455821.93616.25-2.028
126.7698-7.96341.12339.4012-1.31730.19460.32810.74340.69090.1815-0.4057-0.8079-0.75850.31440.03220.65720.01290.00970.6695-0.00190.63729.85515.304-16.214
133.7508-0.42940.21245.28781.64154.7702-0.0851-0.30080.82230.2299-0.12430.0908-0.5461-0.02960.20140.3177-0.0376-0.00270.3554-0.04380.457310.55618.366.426
141.68070.0604-0.47141.577-0.45121.4779-0.0223-0.2565-0.19340.2815-0.058-0.43990.15550.36690.0740.35210.0794-0.08940.4210.06740.494330.316-11.14.906
150.5852-0.2930.2951.9131-0.23841.6441-0.0468-0.1951-0.10220.0049-0.0444-0.59620.11570.54280.0830.33990.08860.06920.61470.08410.778743.102-8.603-11.482
162.55510.7998-0.27094.1169-1.10962.09430.118-0.03960.61730.2889-0.10110.4285-0.5954-0.25270.0150.37540.05730.00760.3539-0.05230.4822-15.21517.101-17.707
171.26373.352.39919.57986.92974.98440.2923-0.48710.4699-0.17390.1789-0.3739-0.3806-0.6545-0.41840.55630.0103-0.01560.6002-0.01360.6937-2.05113.672-4.436
183.1494-0.63070.08716.3768-0.44914.6317-0.0025-0.00170.6787-0.3772-0.2530.1217-0.5304-0.03690.2260.33820.0193-0.01310.28590.03390.394-4.35422.817-25.109
192.3740.0739-0.60261.49480.49321.141-0.06330.5068-0.2255-0.4624-0.1150.3294-0.0454-0.35350.17290.5228-0.0249-0.14440.4956-0.09080.3435-16.595-11.069-39.328
201.8130.2273-0.20752.7835-0.48561.6192-0.0010.09740.1607-0.168-0.08060.68720.0087-0.48920.07370.3129-0.0237-0.04460.4976-0.13610.5625-30.022-4.976-20.887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:208 )A1 - 208
2X-RAY DIFFRACTION2( CHAIN A AND RESID 209:277 )A209 - 277
3X-RAY DIFFRACTION3( CHAIN A AND RESID 278:343 )A278 - 343
4X-RAY DIFFRACTION4( CHAIN A AND RESID 344:472 )A344 - 472
5X-RAY DIFFRACTION5( CHAIN A AND RESID 488:554 )A488 - 554
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:129 )B1 - 129
7X-RAY DIFFRACTION7( CHAIN B AND RESID 130:215 )B130 - 215
8X-RAY DIFFRACTION8( CHAIN B AND RESID 216:468 )B216 - 468
9X-RAY DIFFRACTION9( CHAIN B AND RESID 469:498 )B469 - 498
10X-RAY DIFFRACTION10( CHAIN B AND RESID 499:554 )B499 - 554
11X-RAY DIFFRACTION11( CHAIN C AND RESID 3:109 )C3 - 109
12X-RAY DIFFRACTION12( CHAIN C AND RESID 110:127 )C110 - 127
13X-RAY DIFFRACTION13( CHAIN C AND RESID 128:210 )C128 - 210
14X-RAY DIFFRACTION14( CHAIN C AND RESID 211:476 )C211 - 476
15X-RAY DIFFRACTION15( CHAIN C AND RESID 477:554 )C477 - 554
16X-RAY DIFFRACTION16( CHAIN D AND RESID 3:108 )D3 - 108
17X-RAY DIFFRACTION17( CHAIN D AND RESID 109:127 )D109 - 127
18X-RAY DIFFRACTION18( CHAIN D AND RESID 128:210 )D128 - 210
19X-RAY DIFFRACTION19( CHAIN D AND RESID 211:387 )D211 - 387
20X-RAY DIFFRACTION20( CHAIN D AND RESID 388:554 )D388 - 554

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