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- PDB-2y76: Structure of Mycobacterium tuberculosis type II dehydroquinase co... -

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Basic information

Entry
Database: PDB / ID: 2y76
TitleStructure of Mycobacterium tuberculosis type II dehydroquinase complexed with (1R,4S,5R)-3-(benzo(b)thiophen-5-ylmethoxy)-2-(benzo(b) thiophen-5-ylmethyl)-1,4,5-trihydroxycyclohex-2-enecarboxylate
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / AMINO ACID BIOSYNTHESIS
Function / homology
Function and homology information


quinate catabolic process / Chorismate via Shikimate Pathway / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytosol
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CB7 / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Fox, G.C. / Tizon, L. / Prazeres, V.F.V. / Lamb, H. / Hawkins, A.R. / Ainsa, J.A. / Castedo, L. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: J. Med. Chem. / Year: 2011
Title: A prodrug approach for improving antituberculosis activity of potent Mycobacterium tuberculosis type II dehydroquinase inhibitors.
Authors: Tizon, L. / Otero, J.M. / Prazeres, V.F. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Ainsa, J.A. / Castedo, L. / Gonzalez-Bello, C.
History
DepositionJan 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4475
Polymers15,6771
Non-polymers7714
Water91951
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules

A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,34215
Polymers47,0303
Non-polymers2,31212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
Buried area5720 Å2
ΔGint-162.1 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.430, 126.430, 126.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-1146-

SO4

21A-1146-

SO4

31A-2008-

HOH

41A-2041-

HOH

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Components

#1: Protein 3-DEHYDROQUINATE DEHYDRATASE / 3-DEHYDROQUINASE / TYPE II DHQASE


Mass: 15676.737 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SK3430
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-CB7 / (1R,4S,5R)-3-(BENZO[b]THIOPHEN-5-YL)METHOXY-2-(BENZO[b]THIOPHEN-5-YL)METHYL-1,4,5-TRIHYDROXYCYCLOHEX-2-ENE-1-CARBOXYLATE


Mass: 482.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H22O6S2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINITIATOR METHIONINE (RESIDUE 1 IN UNIPROT SEQUENCE) IS REMOVED.

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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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5
Details: 33% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5, 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM EDTA, 200 MM SODIUM CHLORIDE 12.5 MM SODIUM ...Details: 33% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5, 50 MM TRIS-HCL PH 7.5, 1 MM 2-MERCAPTOETHANOL, 1 MM EDTA, 200 MM SODIUM CHLORIDE 12.5 MM SODIUM (1R,4S,5R)- -3-(1-BENZOTHIOPHEN-5-YLMETHOXY)-2-(1-BENZOTHIOPHEN-5- YLMETHYL)-1,4,5-TRIHYDROXY-CYCLOHEX-2-ENE-1-CARBOXYLATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2010
Details: FOCUSING MIRRORS ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK- BAEZ GEOMETRY
RadiationMonochromator: HORIZONTALLY DIFFRACTING MONOCHROMATOR SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.5→38 Å / Num. obs: 5918 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0S

1h0s


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.495 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.483 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21129 508 8.6 %RANDOM
Rwork0.157 ---
obs0.16172 5397 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.344 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1029 0 48 51 1128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211115
X-RAY DIFFRACTIONr_bond_other_d0.0010.02710
X-RAY DIFFRACTIONr_angle_refined_deg1.5132.0231523
X-RAY DIFFRACTIONr_angle_other_deg0.913.0041699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9095134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25623.87849
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24515173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.822159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021222
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02202
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6921.5672
X-RAY DIFFRACTIONr_mcbond_other0.0941.5279
X-RAY DIFFRACTIONr_mcangle_it1.28721072
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7083443
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.634 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.217 83 -
Rwork0.173 775 -
obs--100 %

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