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- PDB-2dhq: 3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS -

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Basic information

Entry
Database: PDB / ID: 2dhq
Title3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsPROTEIN (3-DEHYDROQUINATE DEHYDRATASE)
KeywordsDEHYDRATASE / SHIKIMATE PATHWAY / ALPHA/BETA PROTEIN
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
3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsGourley, D.G. / Hawkins, A.R. / Coggins, J.R. / Isaacs, N.W.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: The two types of 3-dehydroquinase have distinct structures but catalyze 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
DepositionJan 29, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 27, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (3-DEHYDROQUINATE DEHYDRATASE)


Theoretical massNumber of molelcules
Total (without water)15,6771
Polymers15,6771
Non-polymers00
Water2,216123
1
A: PROTEIN (3-DEHYDROQUINATE DEHYDRATASE)
x 10


Theoretical massNumber of molelcules
Total (without water)156,76710
Polymers156,76710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 operation17_554z,x+1/2,y-1/21
crystal symmetry operation22_655-y+1,z+1/2,-x+1/21
crystal symmetry operation27_555-x+1/2,y,-z+1/21
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 operation45_455y-1/2,z+1/2,x1
2
A: PROTEIN (3-DEHYDROQUINATE DEHYDRATASE)
x 12


Theoretical massNumber of molelcules
Total (without water)188,12112
Polymers188,12112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 operation17_554z,x+1/2,y-1/21
crystal symmetry operation22_655-y+1,z+1/2,-x+1/21
crystal symmetry operation27_555-x+1/2,y,-z+1/21
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 operation38_565-x+1/2,-y+3/2,z1
crystal symmetry operation44_556-z+1/2,x+1/2,-y+11
crystal symmetry operation45_455y-1/2,z+1/2,x1
Buried area25370 Å2
ΔGint-66 kcal/mol
Surface area57810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.680, 127.680, 127.680
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-151-

HOH

21A-165-

HOH

31A-259-

HOH

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Components

#1: Protein PROTEIN (3-DEHYDROQUINATE DEHYDRATASE) / DEHYDROQUINASE


Mass: 15676.737 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Plasmid: PKK44 / Gene (production host): AROQ / Production host: Escherichia coli (E. coli) / Strain (production host): SK3430 / Variant (production host): ARO D-
References: UniProt: P0A4Z6, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.5 %
Crystal growpH: 7.2 / Details: pH 7.20
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
pH: 7.16 / Method: vapor diffusion, sitting drop
Details: Gourley, D.G., (1994) Nature Struct. Biol., 241, 488.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2100 mMTris-HCl1drop
36 %PEG60001reservoir
4100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.89
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 11412 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 19.55 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.44
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 7 / % possible all: 94.6
Reflection
*PLUS
Num. measured all: 37418

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THR: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAP
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1117 10 %RANDOM
Rwork0.1471 ---
obs-11412 97.4 %-
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 0 123 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9882
X-RAY DIFFRACTIONp_mcangle_it3.0123
X-RAY DIFFRACTIONp_scbond_it2.2792
X-RAY DIFFRACTIONp_scangle_it3.6253
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1560.15
X-RAY DIFFRACTIONp_singtor_nbd0.1750.3
X-RAY DIFFRACTIONp_multtor_nbd0.270.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0890.3
X-RAY DIFFRACTIONp_planar_tor3.77
X-RAY DIFFRACTIONp_staggered_tor16.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_chiral_restr0.15
X-RAY DIFFRACTIONp_mcbond_it2
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_mcangle_it3
X-RAY DIFFRACTIONp_scangle_it3

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