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- PDB-6pex: An aldo keto reductase with 2-keto- L-gulonate reductase activity -

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Basic information

Entry
Database: PDB / ID: 6pex
TitleAn aldo keto reductase with 2-keto- L-gulonate reductase activity
Componentsaldo keto reductase
KeywordsOXIDOREDUCTASE / D-isomer-specific 2-hydroxyacid dehydrogenase / L-tartaric acid pathway / 2-keto-L-gulonic acid / Ascorbic acid degradation
Function / homology
Function and homology information


glyoxylate reductase / glyoxylate reductase (NADH) activity / D-lactate dehydrogenase / glyoxylate reductase (NADP+) / hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / D-lactate dehydrogenase activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / NAD binding / cytosol
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyoxylate/hydroxypyruvate/pyruvate reductase 2KGR
Similarity search - Component
Biological speciesVitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.581 Å
AuthorsYong, J. / Crystal, S. / Robert, D.H. / John, B.B.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: An aldo-keto reductase with 2-keto-l-gulonate reductase activity functions in l-tartaric acid biosynthesis from vitamin C inVitis vinifera.
Authors: Jia, Y. / Burbidge, C.A. / Sweetman, C. / Schutz, E. / Soole, K. / Jenkins, C. / Hancock, R.D. / Bruning, J.B. / Ford, C.M.
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aldo keto reductase
B: aldo keto reductase
C: aldo keto reductase
D: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)144,5864
Polymers144,5864
Non-polymers00
Water19,4021077
1
A: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)36,1471
Polymers36,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)36,1471
Polymers36,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)36,1471
Polymers36,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: aldo keto reductase


Theoretical massNumber of molelcules
Total (without water)36,1471
Polymers36,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.050, 85.720, 112.900
Angle α, β, γ (deg.)90.000, 89.910, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
aldo keto reductase


Mass: 36146.605 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vitis vinifera (wine grape) / Gene: VIT_09s0002g04300, VITISV_025327 / Organ: Berry / Production host: Escherichia coli (E. coli) / References: UniProt: A5CAL1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1077 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.26 M ammonium sulfate, 100 mM sodium acetate/acetic acid (pH 4.5), 200 mM sodium chloride.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.58→47.15 Å / Num. obs: 188965 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.064 / Rrim(I) all: 0.121 / Net I/σ(I): 5.6 / Num. measured all: 661190 / Scaling rejects: 99
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 3 % / Rmerge(I) obs: 0.352 / Num. unique obs: 9119 / CC1/2: 0.919 / Rpim(I) all: 0.237 / Rrim(I) all: 0.427 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BAZ

3baz


Resolution: 1.581→27.7 Å / Cross valid method: THROUGHOUT / σ(F): 1.61 / Phase error: 33.62 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2513 9350 4.95 %
Rwork0.2299 179517 -
obs0.2498 188947 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.47 Å2 / Biso mean: 20.9948 Å2 / Biso min: 1.92 Å2
Refinement stepCycle: final / Resolution: 1.581→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9511 0 0 1077 10588
Biso mean---23.33 -
Num. residues----1248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5812-1.60840.45914480.43238734918293
1.6084-1.63770.43514300.40398993942395
1.6377-1.66920.41784560.37759000945695
1.6692-1.70320.38924680.3639004947295
1.7032-1.74020.38164840.35158989947395
1.7402-1.78070.30854560.3268931938795
1.7807-1.82520.34114810.3139012949395
1.8252-1.87450.31164570.30858991944895
1.8745-1.92960.30755130.29598917943094
1.9296-1.99180.28354250.27899067949295
1.9918-2.0630.27444670.26528940940795
2.063-2.14550.30044910.25439003949495
2.1455-2.2430.25384790.25479009948895
2.243-2.36110.29174770.2579007948495
2.3611-2.50870.30264390.25179022946195
2.5087-2.7020.27584330.24759046947995
2.702-2.97310.23475170.2278946946394
2.9731-3.40140.22444660.21029005947194
3.4014-4.27830.21584900.19338997948794
4.2783-19.83380.19064480.17718904935292

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