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- PDB-6gso: Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T1... -

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Basic information

Entry
Database: PDB / ID: 6gso
TitleSulfolobus solfataricus 2-keto-3-deoxygluconate aldolase Y132V,T157C variant
Components2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
KeywordsHYDROLASE / 2-keto-3-deoxygluconate / aldolase / Sulfolobus solfataricus
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 Y132V,T157C variant
Authors: Crennell, S.J. / Danson, M.J. / Royer, S.
History
DepositionJun 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 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 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)132,2079
Polymers131,8374
Non-polymers3705
Water10,773598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11890 Å2
ΔGint-60 kcal/mol
Surface area41960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.024, 144.622, 161.486
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 / 2-keto-3-deoxygluconate (KDG) aldolase


Mass: 32959.164 Da / Num. of mol.: 4 / Mutation: Y132V, T157C
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% PEG4K, 8% isopropanol, 0.1M HEPES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→107.73 Å / Num. obs: 90479 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.046 / Rrim(I) all: 0.068 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4466 / CC1/2: 0.859 / Rpim(I) all: 0.36 / Rrim(I) all: 0.522 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W37

1w37


Resolution: 2→80.743 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.2357 4510 4.99 %
Rwork0.1816 --
obs0.1843 90379 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→80.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9280 0 24 598 9902
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129547
X-RAY DIFFRACTIONf_angle_d1.07812920
X-RAY DIFFRACTIONf_dihedral_angle_d14.065883
X-RAY DIFFRACTIONf_chiral_restr0.061488
X-RAY DIFFRACTIONf_plane_restr0.0081636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.34061720.29752815X-RAY DIFFRACTION100
2.0227-2.04650.33051590.27852859X-RAY DIFFRACTION100
2.0465-2.07150.29831260.26442838X-RAY DIFFRACTION100
2.0715-2.09770.29561220.25842870X-RAY DIFFRACTION100
2.0977-2.12530.33421450.25092886X-RAY DIFFRACTION100
2.1253-2.15440.29531410.23782824X-RAY DIFFRACTION100
2.1544-2.18520.29491450.22452882X-RAY DIFFRACTION100
2.1852-2.21780.28761450.21952830X-RAY DIFFRACTION100
2.2178-2.25250.30071510.21792848X-RAY DIFFRACTION100
2.2525-2.28940.31821590.22072856X-RAY DIFFRACTION100
2.2894-2.32890.25471490.20852826X-RAY DIFFRACTION100
2.3289-2.37130.26141380.20042881X-RAY DIFFRACTION100
2.3713-2.41690.23381510.19522846X-RAY DIFFRACTION100
2.4169-2.46620.28771580.20722857X-RAY DIFFRACTION100
2.4662-2.51980.27451590.20092860X-RAY DIFFRACTION100
2.5198-2.57850.27151580.19532861X-RAY DIFFRACTION100
2.5785-2.6430.23921650.18822806X-RAY DIFFRACTION100
2.643-2.71440.28861440.19972910X-RAY DIFFRACTION100
2.7144-2.79430.26821470.19932825X-RAY DIFFRACTION100
2.7943-2.88450.26231450.18492880X-RAY DIFFRACTION99
2.8845-2.98760.24531730.19232872X-RAY DIFFRACTION100
2.9876-3.10720.23931610.19952853X-RAY DIFFRACTION99
3.1072-3.24860.30171520.20072863X-RAY DIFFRACTION99
3.2486-3.41990.2051540.18862868X-RAY DIFFRACTION99
3.4199-3.63420.20271510.16222877X-RAY DIFFRACTION99
3.6342-3.91480.21611420.15222879X-RAY DIFFRACTION99
3.9148-4.30870.18511670.13932881X-RAY DIFFRACTION98
4.3087-4.93210.1811410.13032810X-RAY DIFFRACTION95
4.9321-6.21360.19151400.15722953X-RAY DIFFRACTION98
6.2136-80.80880.20931500.17222953X-RAY DIFFRACTION94

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