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

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Basic information

Entry
Database: PDB / ID: 9gwu
TitleCrystal structure of sulfoquinovose-1-dehydrogenase from Pseudomonas Putida (sulfo-ED pathway)
ComponentsSulfoquinovose 1-dehydrogenase
KeywordsOXIDOREDUCTASE / sulfoquinovose / sulfoglycolysis / short-chain dehydrogenase/reductase / native structure
Function / homologysulfoquinovose 1-dehydrogenase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / Sulfoquinovose 1-dehydrogenase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
B: Sulfoquinovose 1-dehydrogenase
A: Sulfoquinovose 1-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)58,6462
Polymers58,6462
Non-polymers00
Water3,225179
1
B: Sulfoquinovose 1-dehydrogenase
A: Sulfoquinovose 1-dehydrogenase

B: Sulfoquinovose 1-dehydrogenase
A: Sulfoquinovose 1-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)117,2934
Polymers117,2934
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14060 Å2
ΔGint-73 kcal/mol
Surface area33670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.727, 57.293, 91.267
Angle α, β, γ (deg.)90.00, 93.40, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: apo-SQDH was 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 MIB ...Details: apo-SQDH was 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 MIB (Sodium malonate dibasic monohydrate, Imidazole, Boric acid) buffer pH 7.0 and 25% w/v PEG (polyethylene glycol) 1500.

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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 EIGER2 X 16M / Detector: PIXEL / Date: Oct 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→63.07 Å / Num. obs: 46667 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Χ2: 0.89 / Net I/σ(I): 12.8 / Num. measured all: 312595
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.883 / Num. measured all: 16598 / Num. unique obs: 2440 / CC1/2: 0.761 / Rpim(I) all: 0.362 / Rrim(I) all: 0.956 / Χ2: 0.86 / 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: 1.7→63.07 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.641 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23706 2394 5.1 %RANDOM
Rwork0.1946 ---
obs0.19677 44228 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.591 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20.07 Å2
2--1.57 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.7→63.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 0 179 3972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0123863
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4681.7745244
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.586534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43510581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1660.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022996
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_it2.2291.6582078
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9442.9772595
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6321.9051785
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.02220.025854
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 193 -
Rwork0.285 3243 -
obs--99.25 %
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)
11.4399-0.1397-0.37330.44830.21562.6434-0.00590.1582-0.17020.0147-0.09030.13730.2654-0.79710.09630.0346-0.07660.01770.2436-0.03630.0765-21.0103-5.10134.0682
21.2342-0.2802-0.17730.25420.08272.84830.009-0.26390.06890.0417-0.0077-0.0443-0.12180.3425-0.00130.0228-0.02940.00640.11630.0030.03542.60642.88521.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 260
2X-RAY DIFFRACTION2A2 - 260

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