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- PDB-8vw6: Crystal structure of SsuD -

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Basic information

Entry
Database: PDB / ID: 8vw6
TitleCrystal structure of SsuD
ComponentsAlkanesulfonate monooxygenase
KeywordsFLAVOPROTEIN / desulfonase monooxygenase oxidoreductase
Function / homologyalkanesulfonate monooxygenase / alkanesulfonate monooxygenase activity / : / alkanesulfonate catabolic process / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / Alkanesulfonate monooxygenase
Function and homology information
Biological speciesRhodococcus jostii RHA1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.606 Å
AuthorsCaputo, A.T. / Hu, M. / Scott, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: TBD
Title: Crystral structure of SsuD, a desulfonase protein from Rhodococcus jostii RHA
Authors: Hu, M. / Caputo, A.T. / Scott, C.
History
DepositionJan 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 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: Alkanesulfonate monooxygenase
B: Alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)83,5752
Polymers83,5752
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-22 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.859, 81.631, 299.15
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Alkanesulfonate monooxygenase


Mass: 41787.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii RHA1 (bacteria) / Gene: RHA1_ro01768 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0SFV5, alkanesulfonate monooxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.77 % / Description: Flat square plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25 % w/v PEG 3350 0.2 M Magnesium Chloride 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.606→149.575 Å / Num. obs: 16962 / % possible obs: 88.9 % / Redundancy: 13.2 % / CC1/2: 0.959 / Rmerge(I) obs: 0.589 / Rpim(I) all: 0.166 / Rrim(I) all: 0.612 / Net I/σ(I): 4.9
Reflection shellResolution: 2.606→2.845 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.866 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 848 / CC1/2: 0.603 / Rpim(I) all: 0.57 / Rrim(I) all: 1.954 / % possible all: 31.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5data processing
XDS20230630data reduction
Aimless0.7.13data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.606→149.57 Å / Cor.coef. Fo:Fc: 0.824 / Cor.coef. Fo:Fc free: 0.785 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.439
RfactorNum. reflection% reflectionSelection details
Rfree0.2778 821 -RANDOM
Rwork0.2659 ---
obs0.2664 16962 77.7 %-
Displacement parametersBiso mean: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.5915 Å20 Å20 Å2
2--4.8179 Å20 Å2
3----5.4095 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.606→149.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 0 52 5494
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00710840HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8919530HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3200SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1760HARMONIC5
X-RAY DIFFRACTIONt_it5576HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion718SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact8717SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion15.8
LS refinement shellResolution: 2.61→2.78 Å
RfactorNum. reflection% reflection
Rfree0.2984 18 -
Rwork0.3409 --
obs0.3391 414 11.11 %
Refinement TLS params.

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)
10.72780.39180.27850.10390.05551.22190.040.0126-0.06440.0126-0.06640.0134-0.06440.01340.02640.0032-0.00820.00440.0036-0.0024-0.042212.70824.839-54.2651
20.9885-0.2480.47290.2879-0.17292.6194-0.05950.0528-0.03780.05280.01880.1182-0.03780.11820.0407-0.0965-0.02920.0290.13620.0218-0.231212.6977-5.1577-19.6479
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 346
2X-RAY DIFFRACTION2{ B|* }B1 - 346

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