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- PDB-1nqk: Structural Genomics, Crystal structure of Alkanesulfonate monooxy... -

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Basic information

Entry
Database: PDB / ID: 1nqk
TitleStructural Genomics, Crystal structure of Alkanesulfonate monooxygenase
ComponentsAlkanesulfonate monooxygenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / BETA BARREL / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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: 2.2 Å
AuthorsZhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein Alkanesulfonate monooxygenase from E. Coli
Authors: Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJan 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 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: Alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)41,7831
Polymers41,7831
Non-polymers00
Water2,594144
1
A: Alkanesulfonate monooxygenase

A: Alkanesulfonate monooxygenase

A: Alkanesulfonate monooxygenase

A: Alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)167,1324
Polymers167,1324
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
MethodPQS
2
A: Alkanesulfonate monooxygenase

A: Alkanesulfonate monooxygenase


Theoretical massNumber of molelcules
Total (without water)83,5662
Polymers83,5662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area3900 Å2
ΔGint-20 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.251, 84.251, 234.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThis protein exists as monomer

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Components

#1: Protein Alkanesulfonate monooxygenase / / FMNH2-dependent aliphatic sulfonate monooxygenase / Sulfate starvation-induced protein 6 / SSI6


Mass: 41783.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ycbN / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)star
References: UniProt: P80645, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: P80645, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2M NH4 Acetate, 0.1 M Ma Acetate. 22.5% PEG4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793,0.9791,0.9639
DetectorType: SBC-2 / Detector: CCD / Date: Nov 24, 2002 / Details: Si 111 Channel
RadiationMonochromator: Si 111 Channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97911
30.96391
ReflectionResolution: 2.18→50 Å / Num. all: 22690 / Num. obs: 22467 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.89 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 33.87
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.08 / Num. unique all: 2281 / % possible all: 92.3

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Processing

Software
NameVersionClassification
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 2.2→42.13 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The number of reflections for refinement is greater than the number of reflections for data collection, because in CNS (hlml taget) refinement, the Friedel's pair was treated as two seperated reflections.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1718 5 %RANDOM
Rwork0.201 ---
obs0.201 34502 84.2 %-
all-40976 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8496 Å2 / ksol: 0.363014 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å20 Å2
2--3.68 Å20 Å2
3----7.37 Å2
Refine analyzeLuzzati coordinate error free: 0.36 Å / Luzzati sigma a free: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 0 144 2816
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it0.971.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.312
X-RAY DIFFRACTIONc_scangle_it2.162.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 202 4.9 %
Rwork0.281 3962 -
obs--60.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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