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- PDB-4civ: Crystal structure of Mycobacterium tuberculosis type 2 dehydroqui... -

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Basic information

Entry
Database: PDB / ID: 4civ
TitleCrystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with (1R,4R,5R)-1,4,5-trihydroxy-3-hydroxymethylcyclohex-2-ene-1-carboxylic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / BACTERIAL PROTEINS / INHIBITOR / PROTEIN BINDING / SHIKIMIS ACID PATHWAY / SUBSTRATE SPECIFICITY
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-48P / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Lamb, H. / Hawkins, A.R. / Blanco, B. / Sedes, A. / Peon, A. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: J. Med. Chem. / Year: 2014
Title: Exploring the water-binding pocket of the type II dehydroquinase enzyme in the structure-based design of inhibitors.
Authors: Blanco, B. / Sedes, A. / Peon, A. / Otero, J.M. / van Raaij, M.J. / Thompson, P. / Hawkins, A.R. / Gonzalez-Bello, C.
History
DepositionDec 17, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _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 / 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)15,8812
Polymers15,6771
Non-polymers2041
Water39622
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)190,57124
Polymers188,12112
Non-polymers2,45012
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 area25700 Å2
ΔGint-42.1 kcal/mol
Surface area56300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.180, 126.180, 126.180
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-2007-

HOH

21A-2009-

HOH

31A-2015-

HOH

41A-2022-

HOH

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Components

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


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): K-12 / Variant (production host): SK3430
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical ChemComp-48P / (1R,4R,5R)-1,4,5-trihydroxy-3-hydroxymethylcyclohex-2-ene-1-carboxylic acid


Mass: 204.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.8 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growpH: 7.5
Details: 32% (V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.3 M AMMONIUM SULFATE, 0.1 M 4-(2-HYDROXYETHYL)-PIPERAZINE-1-ETHANESULFONIC ACID SODIUM SALT (HEPES) 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: Nov 28, 2012 / Details: PT COATED SI MIRROR
RadiationMonochromator: HORIZONTALLY DIFFRACTING MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→38 Å / Num. obs: 3103 / % possible obs: 81.8 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 37.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 71

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y71

2y71


Resolution: 2.9→36.45 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.873 / SU B: 22.233 / SU ML: 0.394 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY GAP BY DISORDERED REGION BETWEEN ARG-19 AND GLY-25 INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY GAP BY DISORDERED REGION BETWEEN ARG-19 AND GLY-25 INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF APO- CRYSTALS IN INHIBITOR SOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.27937 141 4.5 %RANDOM
Rwork0.21241 ---
obs0.21537 2958 81.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.937 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 14 22 1074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191067
X-RAY DIFFRACTIONr_bond_other_d0.0020.021053
X-RAY DIFFRACTIONr_angle_refined_deg1.051.9741452
X-RAY DIFFRACTIONr_angle_other_deg0.7453.0032400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4325135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42523.19147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26515171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9551510
X-RAY DIFFRACTIONr_chiral_restr0.0540.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021209
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
X-RAY DIFFRACTIONr_nbd_refined0.2140.2250
X-RAY DIFFRACTIONr_nbd_other0.1750.21034
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2513
X-RAY DIFFRACTIONr_nbtor_other0.0790.2697
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0733.841067
X-RAY DIFFRACTIONr_mcbond_other0.1543.8511053
X-RAY DIFFRACTIONr_mcangle_it1.9015.7331452
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.67638.5281966
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8365.7662400
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: 2.901→3.058 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.405 26 -
Rwork0.299 355 -
obs--70.04 %

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