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- PDB-4b6q: Structure of Mycobacterium tuberculosis Type II Dehydroquinase in... -

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Basic information

Entry
Database: PDB / ID: 4b6q
TitleStructure of Mycobacterium tuberculosis Type II Dehydroquinase inhibited by (2R)-2-(benzothiophen-5-yl)methyl-3-dehydroquinic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE
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-BZ5 / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 27, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Non-polymer description
Revision 1.3Jan 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 1.4Dec 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)16,6869
Polymers15,6771
Non-polymers1,0098
Water2,324129
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)200,226108
Polymers188,12112
Non-polymers12,10696
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_545-y,z-1/2,-x+1/21
crystal symmetry operation30_455z-1/2,-x,-y+1/21
crystal symmetry operation21_545y,z-1/2,x+1/21
crystal symmetry operation29_455z-1/2,x,y+1/21
crystal symmetry operation31_555-z+1/2,-x,y+1/21
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation32_555-z+1/2,x,-y+1/21
crystal symmetry operation23_555y,-z+1/2,-x+1/21
crystal symmetry operation24_555-y,-z+1/2,x+1/21
Buried area40860 Å2
ΔGint-1205.7 kcal/mol
Surface area55950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.267, 126.267, 126.267
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-2077-

HOH

41A-2079-

HOH

51A-2095-

HOH

61A-2115-

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-BZ5 / (1R,2R,4S,5R)-2-(benzo[b]thiophen-5-yl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid


Mass: 336.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16O6S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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 SODIUM SALT), PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2010 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.55→38 Å / Num. obs: 24676 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0S

1h0s


Resolution: 1.54→38.07 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.056 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.16556 1296 5.3 %RANDOM
Rwork0.13454 ---
obs0.1362 23379 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.547 Å2
Refinement stepCycle: LAST / Resolution: 1.54→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 58 129 1210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211147
X-RAY DIFFRACTIONr_bond_other_d0.0010.02735
X-RAY DIFFRACTIONr_angle_refined_deg1.5642.0091571
X-RAY DIFFRACTIONr_angle_other_deg1.0173.0021783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.445133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92623.39653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46915190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.9851511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02211
X-RAY DIFFRACTIONr_nbd_refined0.2350.2218
X-RAY DIFFRACTIONr_nbd_other0.1820.2739
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2527
X-RAY DIFFRACTIONr_nbtor_other0.0870.2566
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.230
X-RAY DIFFRACTIONr_symmetry_hbond_other0.480.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5881.5677
X-RAY DIFFRACTIONr_mcbond_other0.4571.5276
X-RAY DIFFRACTIONr_mcangle_it2.49321099
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7723470
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6274.5472
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.52231882
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.623 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.217 178 -
Rwork0.176 3387 -
obs--99.61 %

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