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- PDB-6h2r: Sulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D1... -

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Basic information

Entry
Database: PDB / ID: 6h2r
TitleSulfolobus solfataricus 2-keto-3-deoxygluconate aldolase T157V/D181Q/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
ISOPROPYL ALCOHOL / TRIETHYLENE GLYCOL / 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase / 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: 1.574 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/D181Q/A198L variant
Authors: Crennell, S.J. / Danson, M.J. / Royer, S.
History
DepositionJul 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 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 13, 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)133,54319
Polymers132,2974
Non-polymers1,24615
Water22,9871276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14790 Å2
ΔGint-42 kcal/mol
Surface area41330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.352, 86.906, 91.982
Angle α, β, γ (deg.)90.00, 95.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 33074.312 Da / Num. of mol.: 4 / Mutation: T157V, D181Q, 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, UniProt: Q97U28*PLUS, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase

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Non-polymers , 5 types, 1291 molecules

#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1276 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 6.1, 11% PEG4K, 4% isopropanol. Crystal soaked in the same solution with 40mM 2-keto, 3-deoxy-galactonate and 20% glycerol for 2 minutes prior to data collection

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 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: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.57→63.02 Å / Num. obs: 161665 / % possible obs: 97.9 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.032 / Rrim(I) all: 0.063 / Net I/σ(I): 12.6
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.405 / Num. unique obs: 7218 / CC1/2: 0.784 / Rpim(I) all: 0.259 / Rrim(I) all: 0.483 / % possible all: 88.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W37

1w37


Resolution: 1.574→61.584 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.175 8108 5.02 %
Rwork0.1477 --
obs0.1491 161621 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.574→61.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9309 0 82 1276 10667
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910290
X-RAY DIFFRACTIONf_angle_d0.91113986
X-RAY DIFFRACTIONf_dihedral_angle_d12.9386367
X-RAY DIFFRACTIONf_chiral_restr0.0561569
X-RAY DIFFRACTIONf_plane_restr0.0071803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5742-1.59210.29142480.24954406X-RAY DIFFRACTION85
1.5921-1.61080.26172320.22565165X-RAY DIFFRACTION98
1.6108-1.63050.2372550.20915066X-RAY DIFFRACTION97
1.6305-1.65110.23092830.20045118X-RAY DIFFRACTION98
1.6511-1.67280.2222670.195098X-RAY DIFFRACTION98
1.6728-1.69570.20962630.19095140X-RAY DIFFRACTION98
1.6957-1.720.23722300.1875120X-RAY DIFFRACTION98
1.72-1.74560.21882530.18365121X-RAY DIFFRACTION98
1.7456-1.77290.232650.18265191X-RAY DIFFRACTION98
1.7729-1.8020.20162570.17415097X-RAY DIFFRACTION98
1.802-1.83310.20982710.1735165X-RAY DIFFRACTION98
1.8331-1.86640.22112670.17345095X-RAY DIFFRACTION98
1.8664-1.90230.2112740.16525139X-RAY DIFFRACTION99
1.9023-1.94110.20852770.16835109X-RAY DIFFRACTION99
1.9411-1.98330.20122760.16375167X-RAY DIFFRACTION99
1.9833-2.02950.18272590.15565151X-RAY DIFFRACTION99
2.0295-2.08020.18253030.15635111X-RAY DIFFRACTION99
2.0802-2.13650.19622840.15085156X-RAY DIFFRACTION99
2.1365-2.19940.17542720.14585141X-RAY DIFFRACTION99
2.1994-2.27040.17372810.13785170X-RAY DIFFRACTION99
2.2704-2.35150.15482860.13325148X-RAY DIFFRACTION99
2.3515-2.44570.15922930.13685120X-RAY DIFFRACTION99
2.4457-2.5570.18782720.13425240X-RAY DIFFRACTION99
2.557-2.69180.16072630.13135205X-RAY DIFFRACTION99
2.6918-2.86040.15212660.13225210X-RAY DIFFRACTION99
2.8604-3.08130.15162620.13095238X-RAY DIFFRACTION99
3.0813-3.39130.15972930.13535209X-RAY DIFFRACTION99
3.3913-3.8820.15542900.12765148X-RAY DIFFRACTION98
3.882-4.89060.14162880.12055111X-RAY DIFFRACTION97
4.8906-61.63120.16692780.16784958X-RAY DIFFRACTION93

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