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

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Basic information

Entry
Database: PDB / ID: 9gwv
TitleCrystal structure of sulfoquinovose-1-dehydrogenase from Pseudomonas Putida in complex with NAD+ (sulfo-ED pathway)
ComponentsSulfoquinovose 1-dehydrogenase
KeywordsOXIDOREDUCTASE / sulfoquinovose / sulfoglycolysis / short-chain dehydrogenase-reductase / NAD 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,9734
Polymers58,6462
Non-polymers1,3272
Water1,874104
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)119,9468
Polymers117,2934
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area18200 Å2
ΔGint-92 kcal/mol
Surface area31140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.893, 57.021, 91.609
Angle α, β, γ (deg.)90.00, 93.45, 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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 33.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: . SQDH-NAD complex was achieved using co-crystallization, which was obtained from protein solution at 20 mg/mL in 50 mM TRIS buffer, 300 mM NaCl buffer pH 7.5 used to set up a drop ...Details: . SQDH-NAD complex was achieved using co-crystallization, which was obtained from protein solution at 20 mg/mL in 50 mM TRIS buffer, 300 mM NaCl buffer pH 7.5 used to set up a drop containing 0.1 uL protein: 0.15 uL mother liquor, the latter comprising 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES buffer pH 7.5, 25% v/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→46.95 Å / Num. obs: 33641 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.041 / Rrim(I) all: 0.104 / Χ2: 0.84 / Net I/σ(I): 10.2 / Num. measured all: 212809
Reflection shellResolution: 1.9→1.94 Å / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.616 / Num. measured all: 13169 / Num. unique obs: 2154 / CC1/2: 0.962 / Rpim(I) all: 0.275 / Rrim(I) all: 0.676 / Χ2: 0.78 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
xia2data reduction
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→46.95 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.731 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24208 1654 4.9 %RANDOM
Rwork0.1949 ---
obs0.1972 31971 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.283 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å2-0 Å22.04 Å2
2--0.81 Å20 Å2
3---0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3666 0 88 104 3858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0123820
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5871.7735194
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5965505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.129532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98110558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1810.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022912
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_it2.7661.9742026
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.393.5222526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0762.1791794
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.88423.825829
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
Rfree0.364 125 -
Rwork0.345 2321 -
obs--99.8 %
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)
11.276-0.0993-0.36330.4127-0.11473.02940.0006-0.28680.08970.06670.0468-0.0601-0.0330.3455-0.04740.01670.0038-0.01610.0917-0.02820.02375.1796-24.711-24.189
21.5236-0.072-0.47240.54440.21412.0616-0.04150.1846-0.07380.0008-0.01120.13270.2115-0.59410.05280.0368-0.0661-0.0080.18070.00170.0498-18.3511-31.2459-41.5171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 260
2X-RAY DIFFRACTION2B-2 - 260

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