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- PDB-1h0r: Type II Dehydroquinase from Mycobacterium tuberculosis complexed ... -

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Basic information

Entry
Database: PDB / ID: 1h0r
TitleType II Dehydroquinase from Mycobacterium tuberculosis complexed with 2,3-anhydro-quinic acid
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsDEHYDRATASE / SHIKIMATE PATHWAY / LYASE / AROMATIC 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
2,3 -ANHYDRO-QUINIC ACID / PHOSPHATE ION / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRoszak, A.W. / Robinson, D.A. / Frederickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J.
Citation
Journal: To be Published
Title: Structural Basis for Selectivity of Oxime Based Inhibitors Towards Type II Dehydroquinase from Mycobacterium Tuberculosis
Authors: Robinson, D.A. / Roszak, A.W. / Frederickson, M. / Abell, C. / Coggins, J.R. / Lapthorn, A.J.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: The Two Types of 3-Dehydroquinase Have Distinct Structures But Catalyse the Same Overall Reaction
Authors: Gourley, D.G. / Shrive, A.K. / Polikarpov, I. / Krell, T. / Coggins, J.R. / Hawkins, A.R. / Isaacs, N.W. / Sawyer, L.
History
DepositionJun 27, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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)16,1096
Polymers15,6771
Non-polymers4325
Water2,756153
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)193,30672
Polymers188,12112
Non-polymers5,18560
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation27_555-x+1/2,y,-z+1/21
crystal symmetry operation17_554z,x+1/2,y-1/21
crystal symmetry operation45_455y-1/2,z+1/2,x1
crystal symmetry operation31_564-z+1/2,-x+1,y-1/21
crystal symmetry operation35_465y-1/2,-z+1,-x+1/21
crystal symmetry operation44_556-z+1/2,x+1/2,-y+11
crystal symmetry operation22_655-y+1,z+1/2,-x+1/21
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation16_565x,-y+3/2,-z+1/21
crystal symmetry operation38_565-x+1/2,-y+3/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.879, 126.879, 126.879
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-201-

PO4

21A-203-

CL

31A-2029-

HOH

41A-2100-

HOH

51A-2131-

HOH

61A-2143-

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) / Strain: H37RV / Plasmid: MPET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P36918, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase

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Non-polymers , 5 types, 158 molecules

#2: Chemical ChemComp-FA1 / 2,3 -ANHYDRO-QUINIC ACID


Mass: 174.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O5
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.77 Å3/Da / Density % sol: 55.5 %
Crystal growpH: 8.5 / Details: 15% PEG 8K, 0.2M NA/K PHOSPHATE 0.1M TRIS, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 13, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→70 Å / Num. obs: 43406 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 1.75 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DHQ

2dhq


Resolution: 2.1→72.55 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.59 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 19-23 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.216 901 9.7 %RANDOM
Rwork0.144 ---
obs-8374 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 25 153 1226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211096
X-RAY DIFFRACTIONr_bond_other_d0.0040.021034
X-RAY DIFFRACTIONr_angle_refined_deg2.1911.9711490
X-RAY DIFFRACTIONr_angle_other_deg2.94432381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2445137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1440.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021213
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02213
X-RAY DIFFRACTIONr_nbd_refined0.4060.2210
X-RAY DIFFRACTIONr_nbd_other0.2540.21142
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0920.2670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.321.5685
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.21521094
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1813411
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8614.5396
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→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.256 55
Rwork0.183 537
Refinement TLS params.Method: refined / Origin x: 22.639 Å / Origin y: 64.859 Å / Origin z: 23.611 Å
111213212223313233
T0.0276 Å2-0.0027 Å2-0.01 Å2-0.0072 Å2-0.0123 Å2--0.0292 Å2
L0.5549 °2-0.0249 °20.3768 °2-0.5596 °2-0.1222 °2--0.2794 °2
S0.0499 Å °0.0218 Å °-0.0536 Å °-0.007 Å °-0.0107 Å °0.0241 Å °0.0292 Å °0.0051 Å °-0.0392 Å °

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