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- PDB-8y4b: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bou... -

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Basic information

Entry
Database: PDB / ID: 8y4b
TitleCrystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bound to L-2,4-DKDF and NADH
ComponentsSDR family oxidoreductase
KeywordsOXIDOREDUCTASE / dehydrogenase / Rossmann Fold
Function / homology: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesHerbaspirillum huttiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 30, 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)113,1999
Polymers110,3854
Non-polymers2,8145
Water7,080393
1
A: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2602
Polymers27,5961
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2602
Polymers27,5961
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2602
Polymers27,5961
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4203
Polymers27,5961
Non-polymers8242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.868, 119.541, 129.289
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: 27596.275 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-A1LXB / L-2,4-diketo-3-deoxyfuconate / (2~{S},5~{S})-5-methyl-2-oxidanyl-4-oxidanylidene-oxolane-2-carboxylic acid


Mass: 160.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2 M Sodium acetate, 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: Oct 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→44.32 Å / Num. obs: 110122 / % possible obs: 100 % / Redundancy: 19.57 % / CC1/2: 0.991 / Net I/σ(I): 10.1
Reflection shellResolution: 1.67→1.7 Å / Num. unique obs: 5406 / CC1/2: 0.759

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.67→44.32 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 34.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.317 5466 4.97 %
Rwork0.2662 --
obs0.2688 110022 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 187 393 7786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077549
X-RAY DIFFRACTIONf_angle_d1.00910269
X-RAY DIFFRACTIONf_dihedral_angle_d10.81096
X-RAY DIFFRACTIONf_chiral_restr0.0561230
X-RAY DIFFRACTIONf_plane_restr0.0081306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.45232110.4093443X-RAY DIFFRACTION100
1.69-1.710.44092070.38153421X-RAY DIFFRACTION100
1.71-1.730.42521920.36783422X-RAY DIFFRACTION100
1.73-1.750.39491730.33613432X-RAY DIFFRACTION100
1.75-1.770.3871900.32573440X-RAY DIFFRACTION100
1.77-1.80.38012010.31383455X-RAY DIFFRACTION100
1.8-1.820.39232140.31253363X-RAY DIFFRACTION100
1.82-1.850.37491870.30123484X-RAY DIFFRACTION100
1.85-1.880.38631760.29813436X-RAY DIFFRACTION100
1.88-1.910.36181520.30593502X-RAY DIFFRACTION100
1.91-1.940.41811720.30593440X-RAY DIFFRACTION100
1.94-1.980.3451750.29583478X-RAY DIFFRACTION100
1.98-2.020.39351820.29463456X-RAY DIFFRACTION100
2.02-2.060.3661770.29593446X-RAY DIFFRACTION100
2.06-2.10.34831650.30533486X-RAY DIFFRACTION100
2.1-2.150.38341730.2993459X-RAY DIFFRACTION100
2.15-2.210.33341940.29773474X-RAY DIFFRACTION100
2.21-2.270.36561840.28883469X-RAY DIFFRACTION100
2.27-2.330.37711900.27043459X-RAY DIFFRACTION100
2.33-2.410.29431760.27473470X-RAY DIFFRACTION100
2.41-2.490.32341720.27743492X-RAY DIFFRACTION100
2.49-2.590.32381610.27123510X-RAY DIFFRACTION100
2.59-2.710.28651790.26113504X-RAY DIFFRACTION100
2.71-2.860.31111820.2713506X-RAY DIFFRACTION100
2.86-3.030.30531710.2613524X-RAY DIFFRACTION100
3.03-3.270.2971650.25473533X-RAY DIFFRACTION100
3.27-3.60.26161740.24283554X-RAY DIFFRACTION100
3.6-4.120.28381810.22843553X-RAY DIFFRACTION100
4.12-5.190.24141850.21013602X-RAY DIFFRACTION100
5.19-44.320.25192050.21293743X-RAY DIFFRACTION100

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