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- PDB-6h7r: Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A1... -

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Basic information

Entry
Database: PDB / ID: 6h7r
TitleSulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A198L variant
Components2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
KeywordsLYASE / aldolase
Function / homology
Function and homology information


2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / 2-dehydro-3-deoxy-6-phosphogalactonate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase activity
Similarity search - Function
: / 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
2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCrennell, S.J. / Danson, M.J. / Royer, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: To Be Published
Title: Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/A198L variant
Authors: Crennell, S.J. / Danson, M.J. / Royer, S.
History
DepositionJul 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
B: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
C: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
D: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,5538
Polymers132,2454
Non-polymers3084
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-69 kcal/mol
Surface area42180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.103, 126.039, 126.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase


Mass: 33061.273 Da / Num. of mol.: 4 / Mutation: T157V, A198L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O54288, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: 15% PEG4K, 12% isopropanol, 0.1M HEPES pH 5.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 30037 / % possible obs: 89.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 7.95
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.517 / Num. unique obs: 1419 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W37

1w37


Resolution: 2.8→23.545 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.2338 1523 5.08 %
Rwork0.1873 --
obs0.1897 29982 89.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→23.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9316 0 20 63 9399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049530
X-RAY DIFFRACTIONf_angle_d0.66412892
X-RAY DIFFRACTIONf_dihedral_angle_d15.3255858
X-RAY DIFFRACTIONf_chiral_restr0.0421485
X-RAY DIFFRACTIONf_plane_restr0.0041626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7962-2.88630.30261420.2532527X-RAY DIFFRACTION89
2.8863-2.98920.28961610.22742677X-RAY DIFFRACTION95
2.9892-3.10870.26561600.22622645X-RAY DIFFRACTION94
3.1087-3.24980.2521330.22012701X-RAY DIFFRACTION93
3.2498-3.42070.25471420.20432643X-RAY DIFFRACTION92
3.4207-3.63420.24841290.18482632X-RAY DIFFRACTION91
3.6342-3.91370.25721140.18032596X-RAY DIFFRACTION90
3.9137-4.30540.20271370.15912581X-RAY DIFFRACTION89
4.3054-4.92340.18791390.15122528X-RAY DIFFRACTION87
4.9234-6.18430.24111380.18022478X-RAY DIFFRACTION84
6.1843-23.54560.1811280.17512451X-RAY DIFFRACTION80

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