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- PDB-2pa7: Structure of Wild-Type dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisom... -

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Basic information

Entry
Database: PDB / ID: 2pa7
TitleStructure of Wild-Type dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase from Aneurinibacillus thermoaerophilus in complex with TDP
ComponentsDTDP-6-deoxy-3,4-keto-hexulose isomerase
KeywordsISOMERASE / deoxysugar biosynthesis / S-Layer biosynthesis / ketoisomerase
Function / homology
Function and homology information


TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (dTDP-3-dehydro-6-deoxy-alpha-D-galactopyranose-forming) / isomerase activity
Similarity search - Function
Sugar 3,4-ketoisomerase QdtA, cupin domain / WxcM-like, C-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase
Similarity search - Component
Biological speciesAneurinibacillus thermoaerophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsDavis, M.L. / Thoden, J.B. / Holden, H.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The X-ray Structure of dTDP-4-Keto-6-deoxy-D-glucose-3,4-ketoisomerase.
Authors: Davis, M.L. / Thoden, J.B. / Holden, H.M.
History
DepositionMar 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: DTDP-6-deoxy-3,4-keto-hexulose isomerase
B: DTDP-6-deoxy-3,4-keto-hexulose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,97815
Polymers32,5172
Non-polymers1,46113
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-9 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.725, 61.725, 201.331
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DTDP-6-deoxy-3,4-keto-hexulose isomerase


Mass: 16258.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aneurinibacillus thermoaerophilus (bacteria)
Strain: L420-91T / Gene: fdtA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: Q6T1W8, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20-21% PEG 3400, 150-200mM KCl, 100mM HEPES, 10mM TDP, 20mM fucose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97907, 0.96411, 0.97924, 0.96411
DetectorType: SBC-3 / Detector: CCD / Date: Aug 14, 2006 / Details: mirrors
RadiationMonochromator: Double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.964111
30.979241
ReflectionResolution: 1.5→50 Å / Num. all: 62658 / Num. obs: 62658 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 48.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5740 / Rsym value: 0.524 / % possible all: 92.3

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
TNTrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→50 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 6370 -random
Rwork0.194 ---
all0.195 62623 --
obs0.195 62623 98.7 %-
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 91 389 2683

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