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- PDB-2pak: Structure of a H51N mutant dTDP-4-keto-6-deoxy-D-glucose-3,4-keto... -

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Basic information

Entry
Database: PDB / ID: 2pak
TitleStructure of a H51N mutant dTDP-4-keto-6-deoxy-D-glucose-3,4-ketoisomerase from Aneurinibacillus thermoaerophilus complexed 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)33,2734
Polymers32,4692
Non-polymers8042
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-31 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.3, 61.3, 201.4
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 16234.509 Da / Num. of mol.: 2 / Mutation: H51N
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-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 57.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 18% PEG 3400, 150mM LiCl, 100mM CHES, 10mM TDP, 20mM fucose, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 14, 2007 / Details: Montel
RadiationMonochromator: nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 15617 / Num. obs: 15617 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.0959 / Rsym value: 0.0959 / Net I/σ(I): 15.7
Reflection shellResolution: 2.39→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1595 / Rsym value: 0.422 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
EPMRphasing
TNTrefinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2PA7

2pa7


Resolution: 2.4→30 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1595 -random
Rwork0.207 ---
all0.213 15580 --
obs0.213 15580 97.5 %-
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 50 121 2352

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