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- PDB-3n8n: Crystal structure of 3-dehydroquinate dehydratase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3n8n
TitleCrystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in complex with inhibitor 6
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-N88 / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 28, 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)383,21638
Polymers379,39024
Non-polymers3,82614
Water28,0131555
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)192,70123
Polymers189,69512
Non-polymers3,00611
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25410 Å2
ΔGint-55 kcal/mol
Surface area54950 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)190,51515
Polymers189,69512
Non-polymers8203
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26010 Å2
ΔGint-48 kcal/mol
Surface area57200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.840, 137.520, 148.330
Angle α, β, γ (deg.)90.00, 95.88, 90.00
Int Tables number4
Space group name H-MP1211

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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: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-N88 / (1R,4R,5R)-3-(tert-butylcarbamoyl)-1,4,5-trihydroxycyclohex-2-ene-1-carboxylic acid


Mass: 273.282 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C12H19NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1555 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 298 K / Method: microbath on oil / pH: 7.5
Details: potassium bromate Peg 2000mme, pH 7.5, microbath on oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: 2009 / Details: mirrors
RadiationMonochromator: Si (311) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→62.3 Å / Num. all: 133469 / Num. obs: 115676 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 5.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 1.3 / Num. unique all: 16264 / % possible all: 84

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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: 3N7A

3n7a


Resolution: 2.5→62.3 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.841 / SU B: 12.037 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29528 5817 5 %RANDOM
Rwork0.20114 ---
all0.229 115676 --
obs0.20588 109823 86.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.898 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→62.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24999 0 266 1555 26820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02125656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.97534992
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96853288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37123.6361114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.265154029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.15115208
X-RAY DIFFRACTIONr_chiral_restr0.1020.24211
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02119256
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_it0.6721.516456
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24226158
X-RAY DIFFRACTIONr_scbond_it1.70939200
X-RAY DIFFRACTIONr_scangle_it2.8784.58834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 392 -
Rwork0.274 7829 -
obs--83.74 %

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