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- PDB-3n7a: Crystal structure of 3-dehydroquinate dehydratase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3n7a
TitleCrystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 2
Components3-dehydroquinate dehydratase
KeywordsLYASE/LYASE INHIBITOR / dehydroquinate dehydratase / 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
2,3 -ANHYDRO-QUINIC ACID / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Sep 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)384,76761
Polymers379,39024
Non-polymers5,37737
Water42,2812347
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)192,33830
Polymers189,69512
Non-polymers2,64218
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33980 Å2
ΔGint-35 kcal/mol
Surface area54480 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)192,43031
Polymers189,69512
Non-polymers2,73419
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33980 Å2
ΔGint-35 kcal/mol
Surface area54360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.912, 95.557, 124.470
Angle α, β, γ (deg.)79.93, 80.30, 77.60
Int Tables number1
Space group name H-MP1

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Components

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


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, 3-dehydroquinate dehydratase
#2: Chemical...
ChemComp-FA1 / 2,3 -ANHYDRO-QUINIC ACID


Mass: 174.151 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C7H10O5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2347 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
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: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2007 / Details: mirrors
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2→79.305 Å / Num. all: 269740 / Num. obs: 254550 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Biso Wilson estimate: 25.29 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.069 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.3 / Num. unique all: 37375 / Rsym value: 0.513 / % possible all: 94.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H0R

1h0r


Resolution: 2→79.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.521 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23795 12908 5 %RANDOM
Rwork0.17772 ---
all0.1854 269740 --
obs0.18077 243465 95.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.013 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→79.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25587 0 366 2347 28300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02126504
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0541.97236114
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02153347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5223.1931184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.847154170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.48115238
X-RAY DIFFRACTIONr_chiral_restr0.170.24327
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02119896
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_it1.1751.516691
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.945226639
X-RAY DIFFRACTIONr_scbond_it3.11539813
X-RAY DIFFRACTIONr_scangle_it4.6254.59475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 965 -
Rwork0.302 18054 -
obs--95.12 %

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