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- PDB-4uxd: 2-keto 3-deoxygluconate aldolase from Picrophilus torridus -

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Basic information

Entry
Database: PDB / ID: 4uxd
Title2-keto 3-deoxygluconate aldolase from Picrophilus torridus
Components2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE
KeywordsLYASE / TIM BARREL
Function / homology
Function and homology information


2-dehydro-3-deoxy-6-phosphogalactonate aldolase / 2-dehydro-3-deoxy-D-gluconate aldolase / 2-dehydro-3-deoxy-D-gluconate aldolase activity / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / Lyases; Carbon-carbon lyases; Aldehyde-lyases / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / aldehyde-lyase activity / glucose catabolic process
Similarity search - Function
Schiff base-forming aldolase, active site / Dihydrodipicolinate synthase signature 2. / DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / 2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase
Similarity search - Component
Biological speciesPICROPHILUS TORRIDUS (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPriftis, A. / Zaitsev, V. / Reher, M. / Johnsen, U. / Danson, M.J. / Taylor, G.L. / Schoenheit, P. / Crennell, S.J.
Citation
Journal: Biochemistry / Year: 2018
Title: Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3- ...Title: Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate.
Authors: Zaitsev, V. / Johnsen, U. / Reher, M. / Ortjohann, M. / Taylor, G.L. / Danson, M.J. / Schonheit, P. / Crennell, S.J.
#1: Journal: J.Bacteriol. / Year: 2010
Title: The Nonphosphorylative Entner-Doudoroff Pathway in the Thermoacidophilic Euryarchaeon Picrophilus Torridus Involves a Novel 2-Keto-3-Deoxygluconate- Specific Aldolase.
Authors: Reher, M. / Fuhrer, T. / Bott, M. / Schonheit, P.
History
DepositionAug 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: 2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE
B: 2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE
C: 2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE
D: 2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,88033
Polymers136,3834
Non-polymers2,49729
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16940 Å2
ΔGint-20.3 kcal/mol
Surface area36860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.954, 100.159, 154.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE / 2-DEHYDRO-3-DEOXY-GALACTONATE/2-DEHYDRO-3-DEOXY-6 -PHOSPHOGALACTONATE ALDOLASE / 2-KETO-3- ...2-DEHYDRO-3-DEOXY-GALACTONATE/2-DEHYDRO-3-DEOXY-6 -PHOSPHOGALACTONATE ALDOLASE / 2-KETO-3-DEOXYGLUCONATE ALDOLASE


Mass: 34095.848 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PICROPHILUS TORRIDUS (archaea) / Strain: DSM 9790 / JCM 10055 / NBRC 100828 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIL
References: UniProt: Q6KZI8, 2-dehydro-3-deoxy-D-gluconate aldolase , 2-dehydro-3-deoxy-phosphogluconate aldolase, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase

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Non-polymers , 6 types, 369 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsKDGA_PICTO IS INCOMPLETE.THE SEQUENCE AS DEPOSITED AS Q6KZI8 IS SHORTER THAN THE CORRECT PTO1279 ...KDGA_PICTO IS INCOMPLETE.THE SEQUENCE AS DEPOSITED AS Q6KZI8 IS SHORTER THAN THE CORRECT PTO1279 SEQUENCE BY 8 AMINO ACIDS (AS PUBLISHED IN REHER ET AL. 2010, REFERENCE 1). THE ADDITIONAL 8 AMINO ACIDS ARE MYKGIVCP.

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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: 2.49 Å3/Da / Density % sol: 50.58 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN AT 4.2MG/ML MIXED 1:1 WITH (0.085 M HEPES SODIUM BUFFER PH 7.5, 8.5% V/V 2-PROPANOL, 17% W/V PEG 4000, 15% V/V GLYCEROL (ANHYDROUS))

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: SATURN 944PLUS / Detector: CCD / Date: Mar 26, 2009 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→28.58 Å / Num. obs: 36955 / % possible obs: 86.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.25
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.65 / % possible all: 83.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XKY

1xky


Resolution: 2.5→28.58 Å / SU ML: 0.37 / σ(F): 1.33 / Phase error: 30.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2595 1884 5.1 %
Rwork0.1746 --
obs0.1792 36657 86.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8796 0 163 340 9299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089154
X-RAY DIFFRACTIONf_angle_d1.17912295
X-RAY DIFFRACTIONf_dihedral_angle_d15.3083460
X-RAY DIFFRACTIONf_chiral_restr0.041298
X-RAY DIFFRACTIONf_plane_restr0.0051566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.56770.3191360.22382586X-RAY DIFFRACTION85
2.5677-2.64320.32811610.22132813X-RAY DIFFRACTION92
2.6432-2.72840.35181550.22123024X-RAY DIFFRACTION99
2.7284-2.82590.33111690.20443067X-RAY DIFFRACTION100
2.8259-2.93890.2951520.20463104X-RAY DIFFRACTION100
2.9389-3.07250.3311490.18873074X-RAY DIFFRACTION100
3.0725-3.23430.29771710.19173087X-RAY DIFFRACTION100
3.2343-3.43660.26881750.18423044X-RAY DIFFRACTION99
3.4366-3.70150.2722910.19661490X-RAY DIFFRACTION49
3.7015-4.0730.23931200.16312216X-RAY DIFFRACTION75
4.073-4.66020.18131470.12622640X-RAY DIFFRACTION84
4.6602-5.8630.21761300.13162238X-RAY DIFFRACTION71
5.863-28.58140.2021280.15282390X-RAY DIFFRACTION72

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