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- PDB-1h05: 3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN C... -

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Basic information

Entry
Database: PDB / ID: 1h05
Title3-DEHYDROQUINATE DEHYDRATASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH SULPHATE
Components3-DEHYDROQUINATE DEHYDRATASE
KeywordsDEHYDRATASE / SHIKIMATE PATHWAY / ALPHA/BETA PROTEIN / 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
3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRoszak, A.W. / Coggins, J.R. / Lapthorn, A.J.
Citation
Journal: FEBS Lett. / Year: 2002
Title: Specificity of Substrate Recognition by Type II Dehydroquinases as Revealed by Binding of Polyanions(1)
Authors: Evans, L. / Roszak, A.W. / Noble, L. / Robinson, D. / Chalk, P. / Matthews, J. / Coggins, J.R. / Price, N. / Lapthorn, A.J.
#1: Journal: Nat.Struct.Biol. / Year: 1999
Title: The Two Types of 3-Dehydroquinase Have Different 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
DepositionJun 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)16,0615
Polymers15,6771
Non-polymers3844
Water3,603200
1
A: 3-DEHYDROQUINATE DEHYDRATASE
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)192,73260
Polymers188,12112
Non-polymers4,61148
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)126.635, 126.635, 126.635
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-202-

SO4

21A-202-

SO4

31A-2031-

HOH

41A-2045-

HOH

51A-2127-

HOH

61A-2150-

HOH

71A-2160-

HOH

81A-2178-

HOH

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Components

#1: Protein 3-DEHYDROQUINATE DEHYDRATASE / 3-DEHYDROQUINASE / TYPE 2 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(DE3)
References: UniProt: P36918, UniProt: P9WPX7*PLUS, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES TRANS-DEHYDRATION VIA AN ENOLATE INTERMEDIATE.

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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 %
Description: LOW COMPLETENESS AND REDUNDANCY IN HIGHEST RESOLUTION SHELL AS DATA WERE PROCESSED TO CORNERS OF CCD DETECTOR
Crystal growpH: 7.5 / Details: 30% MPD, 0.5M AMMONIUM SULPHATE 0.1M HEPES PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
230 %MPD1reservoir
30.5 Mammonium sulfate1reservoir
40.1 MHEPES1reservoirpH7.5

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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: Feb 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 24274 / % possible obs: 89.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.3
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.832 / % possible all: 32.7
Reflection
*PLUS
Highest resolution: 1.45 Å / Num. measured all: 85115
Reflection shell
*PLUS
% possible obs: 32.7 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DHQ

2dhq


Resolution: 1.5→30 Å / σ(F): 0 / ESU R: 0.08894 / ESU R Free: 0.07971
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2427 10 %RANDOM
Rwork0.139 ---
obs-24274 89.9 %-
Displacement parametersBiso mean: 20.1 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 20 200 1265
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.025
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1
LS refinement shell
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rwork: 0.1 / Num. reflection Rwork: 1141 / Total num. of bins used: 20

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