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- PDB-2xb8: Structure of Mycobacterium tuberculosis type II dehydroquinase in... -

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Basic information

Entry
Database: PDB / ID: 2xb8
TitleStructure of Mycobacterium tuberculosis type II dehydroquinase in complex with inhibitor compound (2R)-2-(4-methoxybenzyl)-3- dehydroquinic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / AMINO ACID BIOSYNTHESIS
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-XNW / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOtero, J.M. / Tizon, L. / Llamas-Saiz, A.L. / Fox, G.C. / Gonzalez-Bello, C. / van Raaij, M.J.
Citation
Journal: Chemmedchem / Year: 2010
Title: Understanding the Key Factors that Control the Inhibition of Type II Dehydroquinase by (2R)-2- Benzyl-3-Dehydroquinic Acids.
Authors: Peon, A. / Otero, J.M. / Tizon, L. / Prazeres, V.F.V. / Llamas-Saiz, A.L. / Fox, G.C. / van Raaij, M.J. / Lamb, H. / Hawkins, A.R. / Gago, F. / Castedo, L. / Gonzalez-Bello, C.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of a Type II Dehydroquinase from Mycobacterium Tuberculosis.
Authors: Gourley, D.G. / Coggins, J.R. / Isaacs, N.W. / Moore, J.D. / Charles, I.G. / Hawkins, A.R.
#2: Journal: Biochem.J. / Year: 1992
Title: Inducible Overproduction of the Aspergillus Nidulans Pentafunctional Arom Protein and the Type-I and -II 3-Dehydroquinases from Salmonella Typhi and Mycobacterium Tuberculosis.
Authors: Moore, J.D. / Lamb, H.K. / Garbe, T. / Servos, S. / Dougan, G. / Charles, I.G. / Hawkins, A.R.
History
DepositionApr 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Refinement description / Version format compliance
Revision 1.2Feb 7, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)16,78210
Polymers15,6771
Non-polymers1,1059
Water90150
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)201,379120
Polymers188,12112
Non-polymers13,259108
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_545-y,z-1/2,-x+1/21
crystal symmetry operation30_455z-1/2,-x,-y+1/21
crystal symmetry operation31_555-z+1/2,-x,y+1/21
crystal symmetry operation29_455z-1/2,x,y+1/21
crystal symmetry operation21_545y,z-1/2,x+1/21
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation32_555-z+1/2,x,-y+1/21
crystal symmetry operation23_555y,-z+1/2,-x+1/21
crystal symmetry operation24_555-y,-z+1/2,x+1/21
Buried area46570 Å2
ΔGint-1173.5 kcal/mol
Surface area52470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.520, 126.520, 126.520
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-1145-

SO4

21A-1145-

SO4

31A-2008-

HOH

41A-2017-

HOH

51A-2034-

HOH

61A-2041-

HOH

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Components

#1: Protein 3-DEHYDROQUINATE DEHYDRATASE / TYPE II DHQASE / 3-DEHYDROQUINASE


Mass: 15676.737 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SK3430
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-XNW / (1R,2R,4S,5R)-1,4,5-TRIHYDROXY-2-(4-METHOXYBENZYL)-3-OXOCYCLOHEXANECARBOXYLIC ACID / (2R)-2-METHOXYBENZYL-3-DEHYDROQUINIC ACID


Mass: 310.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O7
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5
Details: 20 MG/ML DEHYDROQUINASE, 0.05 M TRIS-HCL PH 7.5, 1 MM EDTA, 0.2 M SODIUM CHLORIDE, 12.5 MM (2R)-2-PARA-METHOXYBENZYL-3-DEHYDROQUINIC ACID, 5% (V/V) METHANOL, 32% (V/V) 2-METHYL-2,4- ...Details: 20 MG/ML DEHYDROQUINASE, 0.05 M TRIS-HCL PH 7.5, 1 MM EDTA, 0.2 M SODIUM CHLORIDE, 12.5 MM (2R)-2-PARA-METHOXYBENZYL-3-DEHYDROQUINIC ACID, 5% (V/V) METHANOL, 32% (V/V) 2-METHYL-2,4-PENTANEDIOL, 0.3 M AMMONIUM SULPHATE, 0.1 M HEPES-NAOH PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2010
Details: ONE PAIR OF (300X40X15) MM3 LONG PT COATED SI MIRROR, 260MM USABLE, IN A KIRKPATRICK-BAEZ GEOMETRY
RadiationMonochromator: HORIZONTALLY SIDE DIFFRACTING SILICON 111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→38 Å / Num. obs: 6707 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 11 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0S

1h0s


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.402 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20594 503 7.5 %RANDOM
Rwork0.15639 ---
obs0.1602 6175 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.109 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 65 50 1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211149
X-RAY DIFFRACTIONr_bond_other_d0.0010.02730
X-RAY DIFFRACTIONr_angle_refined_deg1.5542.0161570
X-RAY DIFFRACTIONr_angle_other_deg0.9793.0021761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3225140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95423.26549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23515174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.531510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02217
X-RAY DIFFRACTIONr_nbd_refined0.2150.2203
X-RAY DIFFRACTIONr_nbd_other0.1870.2715
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2543
X-RAY DIFFRACTIONr_nbtor_other0.0850.2553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8031.5703
X-RAY DIFFRACTIONr_mcbond_other0.1331.5289
X-RAY DIFFRACTIONr_mcangle_it1.46121120
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9553446
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0154.5450
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.401→2.529 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.239 81 -
Rwork0.169 887 -
obs--100 %

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