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- PDB-3n76: Crystal structure of 3-dehydroquinate dehydratase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3n76
TitleCrystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with compound 5
Components3-dehydroquinate dehydratase
KeywordsLYASE/LYASE INHIBITOR / dehydroquinate dehydratase / aroD / shikimate pathway / drug discovery / mycobacterium tuberculosis / LYASE / 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
Chem-CA2 / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDias, M.V.B. / Snee, W.C. / Bromfield, K.M. / Payne, R. / Palaninathan, S.K. / Ciulli, A. / Howard, N.I. / Abell, C. / Sacchettini, J.C. / Blundell, T.L.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural investigation of inhibitor designs targeting 3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis.
Authors: Dias, M.V. / Snee, W.C. / Bromfield, K.M. / Payne, R.J. / Palaninathan, S.K. / Ciulli, A. / Howard, N.I. / Abell, C. / Sacchettini, J.C. / Blundell, T.L.
History
DepositionMay 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Structure summary
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)16,1182
Polymers15,8081
Non-polymers3101
Water2,900161
1
A: 3-dehydroquinate dehydratase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)193,41924
Polymers189,69512
Non-polymers3,72412
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_454-x-1,y,-z-11
crystal symmetry operation4_544x,-y-1,-z-11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_544z,-x-1,-y-11
crystal symmetry operation7_445-z-1,-x-1,y1
crystal symmetry operation8_454-z-1,x,-y-11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_454-y-1,z,-x-11
crystal symmetry operation11_544y,-z-1,-x-11
crystal symmetry operation12_445-y-1,-z-1,x1
Buried area35540 Å2
ΔGint-82 kcal/mol
Surface area53560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.410, 126.410, 126.410
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-163-

HOH

21A-225-

HOH

31A-248-

HOH

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Components

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


Mass: 15807.932 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 / Plasmid: pET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-CA2 / (1S,3R,4R,5S)-1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)CYCLOHEXANECARBOXYLIC ACID / 1,3,4-TRIHYDROXY-5-(3-PHENOXYPROPYL)-CYCLOHEXANE-1-CARBOXYLIC ACID


Mass: 310.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H22O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, pH7.5 peg 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97825 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: 2009
Details: Si(111) monochromator. Mirror 1: Grazing angle 2.8 mrad, vertical focusing. Mir ror 2: vertical and horizontal focusing.
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97825 Å / Relative weight: 1
ReflectionResolution: 1.9→31.6 Å / Num. all: 13318 / Num. obs: 13302 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 17.725 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.121 / Net I/σ(I): 5.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1 / Num. unique all: 1929 / Rsym value: 0.53 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H0R

1h0r


Resolution: 1.9→31.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.987 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22147 654 4.9 %RANDOM
Rwork0.17528 ---
all0.18572 13318 --
obs0.17753 12624 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.439 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1083 0 22 161 1266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211124
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.9831532
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5055142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07823.26549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29515175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6441510
X-RAY DIFFRACTIONr_chiral_restr0.1690.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021851
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3081.5707
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06821128
X-RAY DIFFRACTIONr_scbond_it3.2163417
X-RAY DIFFRACTIONr_scangle_it4.9284.5404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 50 -
Rwork0.259 930 -
obs--100 %

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