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- PDB-2ox1: Archaeal Dehydroquinase -

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Basic information

Entry
Database: PDB / ID: 2ox1
TitleArchaeal Dehydroquinase
Components3-dehydroquinate dehydratase
KeywordsLYASE / (beta-alpha)8 barrel
Function / homology
Function and homology information


3,4-dihydroxybenzoate biosynthetic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
: / 3-dehydroquinate dehydratase type I / Type I 3-dehydroquinase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.33 Å
AuthorsGallagher, D.T. / Smith, N.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure and lability of archaeal dehydroquinase.
Authors: Smith, N.N. / Gallagher, D.T.
History
DepositionFeb 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: 3-dehydroquinate dehydratase
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3188
Polymers88,9494
Non-polymers3684
Water6,936385
1
A: 3-dehydroquinate dehydratase
B: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6594
Polymers44,4752
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3-dehydroquinate dehydratase
D: 3-dehydroquinate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6594
Polymers44,4752
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.363, 96.060, 117.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a dimer. The crystal asymmetric unit contains two biological dimers.

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Components

#1: Protein
3-dehydroquinate dehydratase / 3-dehydroquinase / Type I DHQase


Mass: 22237.307 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: aroD / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O30011, 3-dehydroquinate dehydratase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M ammonium acetate 0.1M sodium acetate 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 31, 2004 / Details: mirrors
RadiationMonochromator: mirror coating / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.33→20 Å / Num. all: 43264 / Num. obs: 43264 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.36 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7
Reflection shellResolution: 2.33→2.41 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 4 / Num. unique all: 4135 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.33→10 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.22 / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27713 2168 5.1 %RANDOM
Rwork0.20468 ---
all0.20828 40343 --
obs0.20828 40343 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.226 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.81 Å20 Å2
3----0.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.271 Å0.343 Å
Refinement stepCycle: LAST / Resolution: 2.33→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6244 0 24 385 6653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226364
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.9918556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09923.117308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.217151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9561568
X-RAY DIFFRACTIONr_chiral_restr0.1160.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024800
X-RAY DIFFRACTIONr_nbd_refined0.2130.22845
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2650.213
X-RAY DIFFRACTIONr_mcbond_it0.8581.54008
X-RAY DIFFRACTIONr_mcangle_it1.21126288
X-RAY DIFFRACTIONr_scbond_it2.13232605
X-RAY DIFFRACTIONr_scangle_it3.3164.52268
LS refinement shellResolution: 2.33→2.387 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 137 -
Rwork0.249 2708 -
obs--92.28 %

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