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- PDB-4b6o: Structure of Mycobacterium tuberculosis Type II Dehydroquinase in... -

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Basic information

Entry
Database: PDB / ID: 4b6o
TitleStructure of Mycobacterium tuberculosis Type II Dehydroquinase inhibited by (2S)-2-(4-methoxy)benzyl-3-dehydroquinic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / INHIBITOR
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-3DQ / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Lence, E. / Tizon, L. / Peon, A. / Prazeres, V.F.V. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: ACS Chem. Biol. / Year: 2013
Title: Mechanistic basis of the inhibition of type II dehydroquinase by (2S)- and (2R)-2-benzyl-3-dehydroquinic acids.
Authors: Lence, E. / Tizon, L. / Otero, J.M. / Peon, A. / Prazeres, V.F. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Gonzalez-Bello, C.
History
DepositionAug 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Jul 24, 2013Group: Non-polymer description
Revision 1.4Jan 17, 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
Revision 1.5Dec 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 / 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)16,3716
Polymers15,6771
Non-polymers6955
Water2,090116
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)196,45572
Polymers188,12112
Non-polymers8,33560
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation23_544y,-z-1/2,-x-1/21
crystal symmetry operation43_445-z-1/2,-x-1/2,y1
crystal symmetry operation48_445-y-1/2,-z-1/2,x1
crystal symmetry operation27_454-x-1/2,y,-z-1/21
crystal symmetry operation5_555z,x,y1
crystal symmetry operation38_445-x-1/2,-y-1/2,z1
crystal symmetry operation34_454-y-1/2,z,-x-1/21
crystal symmetry operation16_544x,-y-1/2,-z-1/21
crystal symmetry operation18_544z,-x-1/2,-y-1/21
crystal symmetry operation9_555y,z,x1
crystal symmetry operation32_454-z-1/2,x,-y-1/21
Buried area35710 Å2
ΔGint-748.3 kcal/mol
Surface area57720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.190, 126.190, 126.190
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-2020-

HOH

41A-2024-

HOH

51A-2074-

HOH

61A-2089-

HOH

71A-2101-

HOH

81A-2107-

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-3DQ / (1R,2S,4S,5R)-2-(4-methoxyphenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid


Mass: 310.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O7
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 32% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULFATE, 0.1 M 4-(2-HYDROXYETHYL)-PIPERAZINE-1-ETHANESULFONIC ACID SODIUM SALT (HEPES) PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 6, 2010 / Details: VERTICALLY BENDED MULTILAYER MIRRORS
RadiationMonochromator: DIAMOND (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2→63.1 Å / Num. obs: 11386 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % 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→38.05 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.592 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.17799 1104 9.7 %RANDOM
Rwork0.14402 ---
obs0.14735 10274 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: 11.739 Å2
Refinement stepCycle: LAST / Resolution: 2→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 42 116 1238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211177
X-RAY DIFFRACTIONr_bond_other_d0.0020.02768
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9971608
X-RAY DIFFRACTIONr_angle_other_deg0.9063.0021856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.895141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13123.21456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94915191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4631512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02226
X-RAY DIFFRACTIONr_nbd_refined0.2230.2237
X-RAY DIFFRACTIONr_nbd_other0.1870.2772
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2558
X-RAY DIFFRACTIONr_nbtor_other0.0830.2566
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2106
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.223
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1530.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9261.5709
X-RAY DIFFRACTIONr_mcbond_other0.1981.5290
X-RAY DIFFRACTIONr_mcangle_it1.61321141
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9823468
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1684.5467
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→2.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.212 151 -
Rwork0.157 1492 -
obs--100 %

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