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

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Basic information

Entry
Database: PDB / ID: 4ciy
TitleCrystal structure of Mycobacterium tuberculosis type 2 dehydroquinase in complex with (1R,4R,5R)-1,4,5-trihydroxy-3-((1R)-1-hydroxy-2- phenyl)ethylcyclohex-2-en-1-carboxylic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / INHIBITOR / PROTEIN BINDING / SHIKIMIS ACID P 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-NDY / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1727
Polymers15,6771
Non-polymers4956
Water1,65792
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)194,05884
Polymers188,12112
Non-polymers5,93772
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation46_445-y-1/2,z-1/2,-x1
crystal symmetry operation16_545x,-y-1/2,-z+1/21
crystal symmetry operation21_545y,z-1/2,x+1/21
crystal symmetry operation36_455-y-1/2,-z,x+1/21
crystal symmetry operation27_455-x-1/2,y,-z+1/21
crystal symmetry operation38_445-x-1/2,-y-1/2,z1
crystal symmetry operation19_545-z,-x-1/2,y+1/21
crystal symmetry operation42_445z-1/2,-x-1/2,-y1
crystal symmetry operation29_455z-1/2,x,y+1/21
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area36680 Å2
ΔGint-887.8 kcal/mol
Surface area49490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.205, 126.205, 126.205
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-2014-

HOH

41A-2020-

HOH

51A-2068-

HOH

61A-2078-

HOH

71A-2087-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 98 molecules

#2: Chemical ChemComp-NDY / (1R,4R,5R)-1,4,5-trihydroxy-3-[(1R)-1-hydroxy-2-phenyl]ethylcyclohex-2-ene-1-carboxylic acid


Mass: 294.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.9 Å3/Da / Density % sol: 57.1 % / 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: ID29 / Wavelength: 0.97908
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2013 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: CHANNEL-CUT SILICON MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.1→44.62 Å / Num. obs: 9857 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

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

2y71


Resolution: 2.1→38.08 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.065 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.15 / 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-18 AND TYR-24 INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. GAP BY DISORDERED REGION BETWEEN ARG-18 AND TYR-24 INHIBITOR INCLUDED IN ENZYME ACTIVE SITE BY SOAKING OF APO- CRYSTALS IN INHIBITOR SOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.19754 472 4.8 %RANDOM
Rwork0.14549 ---
obs0.14802 9359 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.123 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1032 0 30 92 1154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191096
X-RAY DIFFRACTIONr_bond_other_d0.0040.021067
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9821492
X-RAY DIFFRACTIONr_angle_other_deg0.8563.0042435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.78323.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55515174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9031510
X-RAY DIFFRACTIONr_chiral_restr0.0890.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_nbd_refined0.2680.2338
X-RAY DIFFRACTIONr_nbd_other0.1890.21042
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2534
X-RAY DIFFRACTIONr_nbtor_other0.0870.2667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0460.21
X-RAY DIFFRACTIONr_metal_ion_refined0.3570.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3610.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1790.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7923.1911096
X-RAY DIFFRACTIONr_mcbond_other0.6613.2161067
X-RAY DIFFRACTIONr_mcangle_it4.2564.7181492
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.74332.1572000
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1224.7862435
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: 2.1→2.214 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.227 70 -
Rwork0.167 1359 -
obs--100 %

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