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- PDB-1m41: Crystal structure of Escherichia coli alkanesulfonate monooxygena... -

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Basic information

Entry
Database: PDB / ID: 1m41
TitleCrystal structure of Escherichia coli alkanesulfonate monooxygenase SsuD at 2.3 A resolution
ComponentsFMNH2-dependent alkanesulfonate monooxygenase
KeywordsOXIDOREDUCTASE / FMNH2-dependent monooxygenase / SsuD / TIM-barrel / sulfate starvation / sulfur assimilation / desulfonation / alkanesulfonate / oxygenase / monooxygenase
Function / homology
Function and homology information


alkanesulfonate monooxygenase complex / alkanesulfonate monooxygenase / cellular response to sulfur starvation / alkanesulfonate monooxygenase activity / alkanesulfonate catabolic process / response to heat / protein homotetramerization / identical protein binding
Similarity search - Function
Alkanesulphonate monooxygenase, FMN-dependent / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Alkanesulfonate monooxygenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsEichhorn, E. / Davey, C.A. / Sargent, D.F. / Leisinger, T. / Richmond, T.J.
CitationJournal: J.mol.biol. / Year: 2002
Title: Crystal Structure of Escherichia coli Alkanesulfonate Monooxygenase SsuD
Authors: Eichhorn, E. / Davey, C.A. / Sargent, D.F. / Leisinger, T. / Richmond, T.J.
History
DepositionJul 2, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FMNH2-dependent alkanesulfonate monooxygenase
B: FMNH2-dependent alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)83,3042
Polymers83,3042
Non-polymers00
Water5,585310
1
A: FMNH2-dependent alkanesulfonate monooxygenase
B: FMNH2-dependent alkanesulfonate monooxygenase

A: FMNH2-dependent alkanesulfonate monooxygenase
B: FMNH2-dependent alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)166,6084
Polymers166,6084
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)116.350, 140.760, 125.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-249-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, -z+1/2

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Components

#1: Protein FMNH2-dependent alkanesulfonate monooxygenase


Mass: 41651.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ssuD / Plasmid: pET-24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P80645, Oxidoreductases; Acting on the CH-OH group of donors
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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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: 3 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium formate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14-5 mg/mlprotein1drop
21.75 Msodium formate1drop
33.5 Msodium formate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9795
SYNCHROTRONESRF ID14-420.9797, 0.9795, 0.9322
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 30, 2001
ADSC QUANTUM 42CCDApr 30, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.93221
ReflectionResolution: 2.3→25 Å / Num. all: 44869 / Num. obs: 44511 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.41 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6348 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 24.7 Å / Num. obs: 44869 / % possible obs: 97.3 % / Num. measured all: 752595
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→25 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2032 2.4 %random
Rwork0.235 ---
all0.236 88233 --
obs0.236 83304 94.4 %-
Displacement parametersBiso mean: 55.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.49 Å2--
2--9.45 Å2-
3----3.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-6 Å
Luzzati sigma a0.51 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 0 310 5408
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.72
X-RAY DIFFRACTIONc_dihedral_angle_d24.16
X-RAY DIFFRACTIONc_improper_angle_d1.06
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.435 212 2.7 %
Rwork0.393 7604 -
obs-7816 88.1 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 2.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.16
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06

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