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- PDB-8y4j: Crystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bou... -

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Basic information

Entry
Database: PDB / ID: 8y4j
TitleCrystal structure of L-2-keto-3-deoxyfuconate 4-dehydrogenase bound to D-KDP
ComponentsSDR family oxidoreductase
KeywordsOXIDOREDUCTASE / dehydrogenase / Rossmann Fold
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / SDR family oxidoreductase
Similarity search - Component
Biological speciesHerbaspirillum huttiense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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)104,3999
Polymers103,7264
Non-polymers6735
Water13,601755
1
A: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2023
Polymers25,9311
Non-polymers2702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0382
Polymers25,9311
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0802
Polymers25,9311
Non-polymers1481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SDR family oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0802
Polymers25,9311
Non-polymers1481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.785, 112.009, 129.557
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: 25931.482 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum huttiense (bacteria) / Gene: RJN63_08795 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: A0AAE4G800
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-A1LXD / D-2-keto-3-deoxypentonate / (2~{S},4~{S})-2,4-bis(oxidanyl)oxolane-2-carboxylic acid


Mass: 148.114 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
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: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→44.71 Å / Num. obs: 141071 / % possible obs: 99.8 % / Redundancy: 18.17 % / CC1/2: 0.884 / Net I/σ(I): 10.3
Reflection shellResolution: 1.51→1.54 Å / Num. unique obs: 6876 / CC1/2: 0.791

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Processing

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

Resolution: 1.51→44.71 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 7082 5.1 %
Rwork0.1877 --
obs0.1889 138934 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7078 0 45 755 7878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087283
X-RAY DIFFRACTIONf_angle_d19898
X-RAY DIFFRACTIONf_dihedral_angle_d14.7852531
X-RAY DIFFRACTIONf_chiral_restr0.0651200
X-RAY DIFFRACTIONf_plane_restr0.0071279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.530.28692320.27484386X-RAY DIFFRACTION100
1.53-1.550.30062470.24844453X-RAY DIFFRACTION100
1.55-1.560.24932440.22254332X-RAY DIFFRACTION100
1.56-1.580.23712340.21724482X-RAY DIFFRACTION100
1.58-1.60.24892530.20734359X-RAY DIFFRACTION100
1.6-1.630.21762400.19524472X-RAY DIFFRACTION100
1.63-1.650.23582500.20074370X-RAY DIFFRACTION100
1.65-1.670.23422450.19644410X-RAY DIFFRACTION100
1.67-1.70.22422310.1964428X-RAY DIFFRACTION100
1.7-1.730.25492270.2224345X-RAY DIFFRACTION98
1.73-1.760.2862300.24634413X-RAY DIFFRACTION100
1.76-1.790.26222520.23384406X-RAY DIFFRACTION100
1.79-1.820.21522230.20964460X-RAY DIFFRACTION99
1.82-1.860.2252460.19964418X-RAY DIFFRACTION100
1.86-1.90.23542610.20294217X-RAY DIFFRACTION96
1.9-1.950.2652120.21433979X-RAY DIFFRACTION90
1.95-20.23942020.19564423X-RAY DIFFRACTION98
2-2.050.21622590.19394393X-RAY DIFFRACTION99
2.05-2.110.23172530.22024276X-RAY DIFFRACTION96
2.11-2.180.20762210.19684445X-RAY DIFFRACTION100
2.18-2.260.20792140.20654274X-RAY DIFFRACTION95
2.26-2.350.18251970.17794042X-RAY DIFFRACTION90
2.35-2.450.23112210.19354464X-RAY DIFFRACTION99
2.45-2.580.21082480.19164366X-RAY DIFFRACTION98
2.58-2.740.20662270.20044423X-RAY DIFFRACTION98
2.74-2.960.24292450.19274467X-RAY DIFFRACTION99
2.96-3.250.2112350.18234484X-RAY DIFFRACTION99
3.25-3.720.20992620.17354470X-RAY DIFFRACTION99
3.72-4.690.15372320.14274590X-RAY DIFFRACTION99
4.69-44.710.16552390.16084805X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2415-0.03290.12440.32770.25750.5667-0.01470.0255-0.0226-0.03640.03980.00230.02420.16020.00230.11630.01530.01470.165-0.0050.140916.71055.965920.3458
20.17580.36320.00870.25110.19080.9578-0.0273-0.0354-0.00440.14930.01720.00790.21950.0937-0.05150.18550.0814-0.00210.1510.00830.132314.33297.388950.8436
30.2344-0.1550.07210.41870.38510.7792-0.02580.04640.0366-0.22490.00590.0474-0.33050.0499-0.01040.2691-0.0448-0.00980.13160.01860.151410.409635.022819.9692
40.13620.0916-0.16060.68770.07290.3325-0.0261-0.02350.02250.05720.0704-0.0852-0.08740.16530.00220.1435-0.0243-0.02570.1945-0.01850.173321.582636.425447.9853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 254)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 254)
3X-RAY DIFFRACTION3(chain 'C' and resid 6 through 254)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 254)

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