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- PDB-8xwk: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 8xwk
TitleCrystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase from Herbaspillum huttiense (apo form)
ComponentsSDR family oxidoreductase
KeywordsOXIDOREDUCTASE / dehydrogenase / Rossmann Fold
Function / homologyDI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesHerbaspirillum huttiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsAkagashi, M. / Watanabe, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2024
Title: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase reveals a unique binding mode as a alpha-furanosyl hemiketal of substrates.
Authors: Akagashi, M. / Watanabe, S. / Kwiatkowski, S. / Drozak, J. / Terawaki, S. / Watanabe, Y.
History
DepositionJan 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SDR family oxidoreductase
B: SDR family oxidoreductase
C: SDR family oxidoreductase
D: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4497
Polymers104,1304
Non-polymers3183
Water19,4021077
1
A: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)26,0331
Polymers26,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)26,0331
Polymers26,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SDR family oxidoreductase


Theoretical massNumber of molelcules
Total (without water)26,0331
Polymers26,0331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3514
Polymers26,0331
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.761, 112.364, 129.111
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
SDR family oxidoreductase


Mass: 26032.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum huttiense (bacteria) / Gene: E2K99_19890 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0A4P7ABK7
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1077 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M TRIS-HCl pH8.5, 25% PEG4000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→48.39 Å / Num. obs: 239340 / % possible obs: 99.8 % / Redundancy: 19.45 % / CC1/2: 0.999 / Net I/σ(I): 17.6
Reflection shellResolution: 1.27→1.29 Å / Num. unique obs: 23572 / CC1/2: 0.821

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHASERphasing
Cootmodel building
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.27→45 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 12129 5.07 %
Rwork0.1787 --
obs0.1798 239295 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7137 0 21 1077 8235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057501
X-RAY DIFFRACTIONf_angle_d0.83610206
X-RAY DIFFRACTIONf_dihedral_angle_d7.0511119
X-RAY DIFFRACTIONf_chiral_restr0.0791223
X-RAY DIFFRACTIONf_plane_restr0.0071339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.280.29423880.27267510X-RAY DIFFRACTION99
1.28-1.30.29434550.26887354X-RAY DIFFRACTION99
1.3-1.320.28694110.26597448X-RAY DIFFRACTION99
1.32-1.330.26873980.25797486X-RAY DIFFRACTION99
1.33-1.350.24953640.25237477X-RAY DIFFRACTION99
1.35-1.370.27234080.24867540X-RAY DIFFRACTION99
1.37-1.390.25693850.2447498X-RAY DIFFRACTION99
1.39-1.410.2643950.23797460X-RAY DIFFRACTION100
1.41-1.430.25314230.23017524X-RAY DIFFRACTION100
1.43-1.450.22934220.21577504X-RAY DIFFRACTION100
1.45-1.480.21333830.2067539X-RAY DIFFRACTION100
1.48-1.510.22063910.20277513X-RAY DIFFRACTION100
1.51-1.530.21484040.19637564X-RAY DIFFRACTION100
1.53-1.570.20854070.18527528X-RAY DIFFRACTION100
1.57-1.60.21193870.18727565X-RAY DIFFRACTION100
1.6-1.640.1994130.18597500X-RAY DIFFRACTION100
1.64-1.680.20864090.18467580X-RAY DIFFRACTION100
1.68-1.720.22053970.18567552X-RAY DIFFRACTION100
1.72-1.770.21113810.197574X-RAY DIFFRACTION100
1.77-1.830.21534150.19067575X-RAY DIFFRACTION100
1.83-1.90.22243850.18517623X-RAY DIFFRACTION100
1.9-1.970.20644160.18267563X-RAY DIFFRACTION100
1.97-2.060.18874240.17797560X-RAY DIFFRACTION100
2.06-2.170.19124210.17217628X-RAY DIFFRACTION100
2.17-2.310.19214090.16767640X-RAY DIFFRACTION100
2.31-2.490.19353860.17057655X-RAY DIFFRACTION100
2.49-2.740.20614400.16697643X-RAY DIFFRACTION100
2.74-3.130.18923690.1667763X-RAY DIFFRACTION100
3.13-3.950.17933890.15337781X-RAY DIFFRACTION100
3.95-450.16244540.14998019X-RAY DIFFRACTION100

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