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Basic information

Entry
Database: PDB / ID: 4kij
TitleDesign and structural analysis of aromatic inhibitors of type II dehydroquinase dehydratase from Mycobacterium tuberculosis - compound 35c [3,4-dihydroxy-5-(3-nitrophenoxy)benzoic acid]
Components3-dehydroquinate dehydratase
KeywordsLyase/Lyase Inhibitor / dehydratase / Lyase-Lyase Inhibitor complex
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
3,4-dihydroxy-5-(3-nitrophenoxy)benzoic acid / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDias, M.V.B. / Howard, N.G. / Blundell, T.L. / Abell, C.
CitationJournal: Chemmedchem / Year: 2015
Title: Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase from Mycobacterium tuberculosis.
Authors: Howard, N.I. / Dias, M.V. / Peyrot, F. / Chen, L. / Schmidt, M.F. / Blundell, T.L. / Abell, C.
History
DepositionMay 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9253
Polymers16,5991
Non-polymers3272
Water54030
1
A: 3-dehydroquinate dehydratase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)203,10636
Polymers199,18612
Non-polymers3,92024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation16_545x,-y-1/2,-z+1/21
crystal symmetry operation19_545-z,-x-1/2,y+1/21
crystal symmetry operation21_545y,z-1/2,x+1/21
crystal symmetry operation27_455-x-1/2,y,-z+1/21
crystal symmetry operation29_455z-1/2,x,y+1/21
crystal symmetry operation36_455-y-1/2,-z,x+1/21
crystal symmetry operation38_445-x-1/2,-y-1/2,z1
crystal symmetry operation42_445z-1/2,-x-1/2,-y1
crystal symmetry operation46_445-y-1/2,z-1/2,-x1
Buried area27910 Å2
ΔGint-118 kcal/mol
Surface area53650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.980, 126.980, 126.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-313-

HOH

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Components

#1: Protein 3-dehydroquinate dehydratase / 3-dehydroquinase / Type II DHQase


Mass: 16598.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroD, aroQ, MT2612, MTCY159.19, Rv2537c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-KIJ / 3,4-dihydroxy-5-(3-nitrophenoxy)benzoic acid


Mass: 291.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H9NO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, 25% PEG 6000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9716 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2009
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 2.8→44.9 Å / Num. all: 4288 / Num. obs: 4286 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→25.92 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.856 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.22 / SU ML: 0.333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 195 4.6 %RANDOM
Rwork0.1901 ---
obs0.1929 4281 99.63 %-
all-4286 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.94 Å2 / Biso mean: 26.1213 Å2 / Biso min: 2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 22 30 1129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021117
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9821523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6135141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8823.26549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.60115174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1971510
X-RAY DIFFRACTIONr_chiral_restr0.0840.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021855
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 14 -
Rwork0.264 289 -
all-303 -
obs--100 %

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