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- PDB-4v0s: Crystal structure of Mycobacterium tuberculosis Type II Dehydroqu... -

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Basic information

Entry
Database: PDB / ID: 4v0s
TitleCrystal structure of Mycobacterium tuberculosis Type II Dehydroquinase D88N mutant inhibited by a 3-dehydroquinic acid derivative
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsLYASE / BINDING SITES / TYPE 2 DEHYDROQUINASE / 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-2HN / Chem-7HN / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsOtero, J.M. / Llamas-Saiz, A.L. / Santiago, C. / Lamb, H. / Hawkins, A.R. / Maneiro, M. / Peon, A. / Gonzalez-Bello, C. / van Raaij, M.J.
CitationJournal: To be Published
Title: Investigation of the Dehydratation Mechanism Catalyzed by the Type II Dehydroquinase
Authors: Maneiro, M. / Otero, J.M. / Peon, A. / van Raaij, M.J. / Lamb, H. / Hawkings, A.R. / Gonzalez-Bello, C.
History
DepositionSep 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Jan 10, 2024Group: 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 / 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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _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_asym_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_conn.ptnr2_symmetry / _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
B: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8909
Polymers31,3522
Non-polymers1,5397
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-40.6 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.848, 65.187, 94.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-2009-

HOH

21B-2028-

HOH

31B-2033-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 15675.753 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Plasmid: PKK233-2 / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): SK3430
References: UniProt: P9WPX6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase

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Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-2HN / (1R,2S,4S,5R)-2-(2,3,4,5,6-pentafluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid / (1R,2S,4S,5R)-2-(perfluorophenyl)methyl-1,4,5-trihydroxy-3-oxocyclohexane-1-carboxylic acid


Mass: 370.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H11F5O6
#3: Chemical ChemComp-7HN / 3,4-DIHYDROXY-2-[(2,3,4,5,6-PENTAFLUOROPHENYL)METHYL]BENZOIC ACID


Mass: 334.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H7F5O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.99 Å3/Da / Density % sol: 38.27 % / Description: NONE
Crystal growpH: 6.2 / Details: 28% PEG4000, 100 MM NA-CITRATE PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00227
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2014 / Details: PLANE-ELLIPSOIDAL MIRRORS (SI, RH, IR)
RadiationMonochromator: CHANNEL-CUT DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00227 Å / Relative weight: 1
ReflectionResolution: 1.55→94.75 Å / Num. obs: 34076 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 76.2

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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: 1.55→53.71 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.017 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES ARE REFINED INDIVIDUALLY. GAP BY DISORDERED REGION BETWEEN ALA-107 AND HIS-114 IN CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.18931 1701 5 %RANDOM
Rwork0.13524 ---
obs0.13799 32331 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.382 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.55→53.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 101 150 2380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192317
X-RAY DIFFRACTIONr_bond_other_d0.0010.022221
X-RAY DIFFRACTIONr_angle_refined_deg1.4652.0123192
X-RAY DIFFRACTIONr_angle_other_deg0.8113.0025052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36123.81497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.94715356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9131517
X-RAY DIFFRACTIONr_chiral_restr0.0890.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212634
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined0.2520.2640
X-RAY DIFFRACTIONr_nbd_other0.1690.22157
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21136
X-RAY DIFFRACTIONr_nbtor_other0.090.21396
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.080.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.247
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1640.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0830.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.7581.8692317
X-RAY DIFFRACTIONr_mcbond_other4.3391.9292221
X-RAY DIFFRACTIONr_mcangle_it14.8722.7683184
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it14.39819.1724035
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.9622.8295052
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.56634538
X-RAY DIFFRACTIONr_sphericity_free27.883554
X-RAY DIFFRACTIONr_sphericity_bonded11.76954590
LS refinement shellResolution: 1.55→1.634 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.276 212 -
Rwork0.209 3609 -
obs--74.59 %

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