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- PDB-8y46: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bou... -

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Basic information

Entry
Database: PDB / ID: 8y46
TitleCrystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bound to L-KDF or L-2,4-DKDF
ComponentsSDR family oxidoreductase
KeywordsOXIDOREDUCTASE / dehydrogenase / Rossmann Fold
Function / homology: / : / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesHerbaspirillum huttiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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)111,32611
Polymers110,3854
Non-polymers9417
Water16,015889
1
A: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8813
Polymers27,5961
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7562
Polymers27,5961
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8093
Polymers27,5961
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8813
Polymers27,5961
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.508, 113.050, 129.591
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 896 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-A1LXA / L-2-keto-3-deoxyfuconate / (2~{S},4~{S},5~{S})-5-methyl-2,4-bis(oxidanyl)oxolane-2-carboxylic acid


Mass: 162.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: 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: isolated from a natural source / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.2 M Sodium acetate, 0.1 M Tris-HCl pH8.5, 25% PEG 4000

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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: 1.29→44.99 Å / Num. obs: 230393 / % possible obs: 100 % / Redundancy: 17.82 % / CC1/2: 0.998 / Net I/σ(I): 17.1
Reflection shellResolution: 1.29→1.31 Å / Num. unique obs: 198053 / CC1/2: 0.88

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Processing

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

Resolution: 1.29→44.99 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 11441 4.97 %
Rwork0.1788 --
obs0.1797 230260 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.29→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7178 0 63 889 8130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057446
X-RAY DIFFRACTIONf_angle_d0.91610118
X-RAY DIFFRACTIONf_dihedral_angle_d8.6451109
X-RAY DIFFRACTIONf_chiral_restr0.0791218
X-RAY DIFFRACTIONf_plane_restr0.0071310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.30.28013650.25467323X-RAY DIFFRACTION100
1.3-1.320.25984070.24897153X-RAY DIFFRACTION100
1.32-1.340.25913970.24237215X-RAY DIFFRACTION100
1.34-1.350.26393840.24447212X-RAY DIFFRACTION100
1.35-1.370.26073940.23877198X-RAY DIFFRACTION100
1.37-1.390.23663590.23757299X-RAY DIFFRACTION100
1.39-1.410.25413670.22767232X-RAY DIFFRACTION100
1.41-1.430.26013710.22547226X-RAY DIFFRACTION100
1.43-1.450.2253830.2147288X-RAY DIFFRACTION100
1.45-1.480.22133780.20497173X-RAY DIFFRACTION100
1.48-1.50.20773700.19977268X-RAY DIFFRACTION100
1.5-1.530.22723900.19737264X-RAY DIFFRACTION100
1.53-1.560.22033480.19187278X-RAY DIFFRACTION100
1.56-1.590.22113810.18867252X-RAY DIFFRACTION100
1.59-1.630.20673790.1847226X-RAY DIFFRACTION100
1.63-1.660.20623700.19077315X-RAY DIFFRACTION100
1.66-1.70.20823790.1937249X-RAY DIFFRACTION100
1.7-1.750.22543760.1997278X-RAY DIFFRACTION100
1.75-1.80.23293710.20027272X-RAY DIFFRACTION100
1.8-1.860.19473810.19267270X-RAY DIFFRACTION100
1.86-1.930.213850.18527311X-RAY DIFFRACTION100
1.93-20.20334080.18497274X-RAY DIFFRACTION100
2-2.10.1933680.17627312X-RAY DIFFRACTION100
2.1-2.210.18484140.17327244X-RAY DIFFRACTION100
2.21-2.340.18893880.1657325X-RAY DIFFRACTION100
2.34-2.520.19163610.16977372X-RAY DIFFRACTION100
2.53-2.780.19144050.17187337X-RAY DIFFRACTION100
2.78-3.180.18933860.17097421X-RAY DIFFRACTION100
3.18-4.010.17453730.15497496X-RAY DIFFRACTION100
4.01-44.990.15294030.14777736X-RAY DIFFRACTION100

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