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- PDB-9gww: Crystal structure of sulfoquinovose-1-dehydrogenase from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 9gww
TitleCrystal structure of sulfoquinovose-1-dehydrogenase from Pseudomonas Putida in complex with sulfoquinovose substrate (sulfo-ED pathway)
ComponentsSulfoquinovose 1-dehydrogenase
KeywordsOXIDOREDUCTASE / sulfoquinovose / sulfoglycolysis / sulfosugar / short-chain dehydrogenase-reductase / enzyme-substrate complex
Function / homology
Function and homology information


sulfoquinovose 1-dehydrogenase / oxidoreductase activity
Similarity search - Function
PKS_KR / 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
6-deoxy-6-sulfo-beta-D-glucopyranose / Sulfoquinovose 1-dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003805/1 United Kingdom
CitationJournal: Biochem.J. / Year: 2025
Title: Structure, kinetics, and mechanism of Pseudomonas putida sulfoquinovose dehydrogenase, the first enzyme in the sulfoglycolytic Entner-Doudoroff pathway.
Authors: Burchill, L. / Sharma, M. / Soler, N.M. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J.
History
DepositionSep 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfoquinovose 1-dehydrogenase
B: Sulfoquinovose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8903
Polymers58,6462
Non-polymers2441
Water2,324129
1
A: Sulfoquinovose 1-dehydrogenase
B: Sulfoquinovose 1-dehydrogenase
hetero molecules

A: Sulfoquinovose 1-dehydrogenase
B: Sulfoquinovose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,7816
Polymers117,2934
Non-polymers4882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area13560 Å2
ΔGint-72 kcal/mol
Surface area32160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.869, 57.290, 91.979
Angle α, β, γ (deg.)90.00, 93.12, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Sulfoquinovose 1-dehydrogenase / SQ dehydrogenase


Mass: 29323.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: PpSQ1_00405 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DOV5, sulfoquinovose 1-dehydrogenase
#2: Sugar ChemComp-YZT / 6-deoxy-6-sulfo-beta-D-glucopyranose


Type: saccharide / Mass: 244.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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 % sol: 33.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Binary SQDH-SQ complex was obtained by soaking the sulfonate ligand on a crystal of apo_SQ grown using a 20 mg/mL protein solution in 50 mM TRIS buffer pH 7.5 containing 300 mM NaCl in a ...Details: Binary SQDH-SQ complex was obtained by soaking the sulfonate ligand on a crystal of apo_SQ grown using a 20 mg/mL protein solution in 50 mM TRIS buffer pH 7.5 containing 300 mM NaCl in a drop with 0.15 uL protein: 0.15 uL mother liquor, the latter comprising 0.1 M Magnesium formate dihydrate and 15% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→63.21 Å / Num. obs: 33364 / % possible obs: 97.8 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Χ2: 0.94 / Net I/σ(I): 11.8 / Num. measured all: 209259
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 99.5 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.764 / Num. measured all: 12795 / Num. unique obs: 2182 / CC1/2: 0.815 / Rpim(I) all: 0.343 / Rrim(I) all: 0.839 / Χ2: 0.83 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.66 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.624 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27845 1645 4.9 %RANDOM
Rwork0.2265 ---
obs0.22906 31712 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.661 Å2
Baniso -1Baniso -2Baniso -3
1--3.03 Å20 Å20.35 Å2
2--4.31 Å20 Å2
3----1.31 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3674 0 15 129 3818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.711.775076
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5365508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.131528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38110549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7533.5732043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.8526.3992546
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6473.7141700
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.11541.915706
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 127 -
Rwork0.375 2360 -
obs--99.52 %

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