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- PDB-3n86: Crystal structure of 3-dehydroquinate dehydratase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3n86
TitleCrystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 4
Components3-dehydroquinate dehydratase
KeywordsLYASE/LYASE INHIBITOR / dehydroquinate dehydratase / aroD / Mycobacterium tuberculosis / shikimate pathway / drug discovery / 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-RJP / 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 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
G: 3-dehydroquinate dehydratase
H: 3-dehydroquinate dehydratase
I: 3-dehydroquinate dehydratase
J: 3-dehydroquinate dehydratase
K: 3-dehydroquinate dehydratase
L: 3-dehydroquinate dehydratase
M: 3-dehydroquinate dehydratase
N: 3-dehydroquinate dehydratase
O: 3-dehydroquinate dehydratase
P: 3-dehydroquinate dehydratase
Q: 3-dehydroquinate dehydratase
R: 3-dehydroquinate dehydratase
S: 3-dehydroquinate dehydratase
T: 3-dehydroquinate dehydratase
U: 3-dehydroquinate dehydratase
V: 3-dehydroquinate dehydratase
W: 3-dehydroquinate dehydratase
X: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,05448
Polymers379,39024
Non-polymers7,66324
Water73,9524105
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
E: 3-dehydroquinate dehydratase
F: 3-dehydroquinate dehydratase
G: 3-dehydroquinate dehydratase
H: 3-dehydroquinate dehydratase
I: 3-dehydroquinate dehydratase
J: 3-dehydroquinate dehydratase
K: 3-dehydroquinate dehydratase
L: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,52724
Polymers189,69512
Non-polymers3,83212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27270 Å2
ΔGint-49 kcal/mol
Surface area53580 Å2
MethodPISA
2
M: 3-dehydroquinate dehydratase
N: 3-dehydroquinate dehydratase
O: 3-dehydroquinate dehydratase
P: 3-dehydroquinate dehydratase
Q: 3-dehydroquinate dehydratase
R: 3-dehydroquinate dehydratase
S: 3-dehydroquinate dehydratase
T: 3-dehydroquinate dehydratase
U: 3-dehydroquinate dehydratase
V: 3-dehydroquinate dehydratase
W: 3-dehydroquinate dehydratase
X: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,52724
Polymers189,69512
Non-polymers3,83212
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27240 Å2
ΔGint-42 kcal/mol
Surface area54060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.240, 143.976, 148.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ...
3-dehydroquinate dehydratase


Mass: 15807.932 Da / Num. of mol.: 24
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
#2: Chemical...
ChemComp-RJP / (1R,5R)-1,5-dihydroxy-4-oxo-3-[3-oxo-3-(phenylamino)propyl]cyclohex-2-ene-1-carboxylic acid


Mass: 319.309 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C16H17NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4105 / 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: 52.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes pH 7.5 peg 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: 2008 / Details: mirrors
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→56.5 Å / Num. all: 301028 / Num. obs: 277602 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.081 / Rsym value: 0.069 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.4 / Num. unique all: 39595 / Rsym value: 0.334 / % possible all: 90.4

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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: 3n7a

3n7a


Resolution: 1.9→56.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.999 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21203 14004 5 %RANDOM
Rwork0.15549 ---
all0.171 301028 --
obs0.15835 263571 92.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.211 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→56.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25771 0 552 4105 30428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02126788
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.98736512
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26453372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65423.2941181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.269154189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.06815240
X-RAY DIFFRACTIONr_chiral_restr0.1490.24283
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02120440
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_it1.1921.516781
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.954226771
X-RAY DIFFRACTIONr_scbond_it3.287310007
X-RAY DIFFRACTIONr_scangle_it5.1424.59740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 1032 -
Rwork0.21 19055 -
obs--90.48 %

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