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Basic information

Entry
Database: PDB / ID: 4kiu
TitleDesign and structural analysis of aromatic inhibitors of type II dehydroquinate dehydratase from Mycobacterium tuberculosis - compound 49d [5-[(3-nitrobenzyl)oxy]benzene-1,3-dicarboxylic 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
Chem-KIU / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
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)405,01446
Polymers398,03524
Non-polymers6,98022
Water13,709761
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)202,82424
Polymers199,01712
Non-polymers3,80712
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)202,19022
Polymers199,01712
Non-polymers3,17310
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.410, 139.150, 143.290
Angle α, β, γ (deg.)90.000, 96.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 16584.789 Da / Num. of mol.: 24 / Fragment: aroD
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-KIU / 5-[(3-nitrobenzyl)oxy]benzene-1,3-dicarboxylic acid


Mass: 317.250 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C15H11NO7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 761 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.8
Details: 0.15M KBr, 30% 5000mme, pH 7.8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9791 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: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→142.722 Å / Num. all: 142809 / Num. obs: 142809 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rsym value: 0.173 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.532.50.8670.749885200000.86793.5
2.53-2.682.50.66148312191110.6694.5
2.68-2.872.60.4851.446776182580.48596
2.87-3.12.60.3531.844873172140.35397.4
3.1-3.392.70.2053.243955161070.20598.7
3.39-3.792.90.134542078146730.13499.5
3.79-4.382.90.0947.137663130730.09499.9
4.38-5.373.10.079.333876110340.0799.8
5.37-7.593.50.0877.63000585680.087100
7.59-47.0563.50.03715.91672747710.03799.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.28 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.65 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.497 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 6962 5 %RANDOM
Rwork0.1902 ---
obs0.1939 139255 95.03 %-
all-142809 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.38 Å2 / Biso mean: 29.9535 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25703 0 506 761 26970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226667
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.98336320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98553361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60423.3131174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.216154170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.97515235
X-RAY DIFFRACTIONr_chiral_restr0.1160.24226
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120430
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 504 -
Rwork0.259 9362 -
all-9866 -
obs--92.42 %

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