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- PDB-1g8j: CRYSTAL STRUCTURE ANALYSIS OF ARSENITE OXIDASE FROM ALCALIGENES F... -

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Entry
Database: PDB / ID: 1g8j
TitleCRYSTAL STRUCTURE ANALYSIS OF ARSENITE OXIDASE FROM ALCALIGENES FAECALIS
Components(ARSENITE OXIDASE) x 2
KeywordsOXIDOREDUCTASE / OXIDASE / ARSENITE / MOLYBDOPTERIN / [3Fe-4S] CLUSTER / [2Fe-2S] CLUSTER / RIESKE
Function / homologyRieske 3Fe-4S / Arsenite oxidase, small subunit / Twin arginine translocation (Tat) signal profile. / Rieske [2Fe-2S] iron-sulfur domain profile. / Molydopterin dinucleotide binding domain / Molybdopterin oxidoreductase / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Rieske [2Fe-2S] iron-sulphur domain ...Rieske 3Fe-4S / Arsenite oxidase, small subunit / Twin arginine translocation (Tat) signal profile. / Rieske [2Fe-2S] iron-sulfur domain profile. / Molydopterin dinucleotide binding domain / Molybdopterin oxidoreductase / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Rieske [2Fe-2S] iron-sulphur domain / Rieske iron-sulphur protein / Arsenite oxidase, large subunit / Aspartate decarboxylase-like domain superfamily / Molybdopterin dinucleotide-binding domain / Molybdopterin oxidoreductase / Twin-arginine translocation pathway, signal sequence / Rieske iron-sulphur protein, C-terminal / arsenate reductase (azurin) activity / arsenate reductase (azurin) / oxidoreductase activity, acting on diphenols and related substances as donors / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / 2 iron, 2 sulfur cluster binding / membrane / metal ion binding / Arsenite oxidase subunit AioB / Arsenite oxidase subunit AioA
Function and homology information
Specimen sourceAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 2.03 Å resolution
AuthorsEllis, P.J. / Conrads, T. / Hille, R. / Kuhn, P.
Citation
Journal: Structure / Year: 2001
Title: Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 A and 2.03 A.
Authors: Ellis, P.J. / Conrads, T. / Hille, R. / Kuhn, P.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: The purification and characterization of arsenite oxidase from Alcaligenes faecalis, a molybdenum-containing hydroxylase
Authors: Anderson, G.L. / Williams, J. / Hille, R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 17, 2000 / Release: Dec 13, 2000
RevisionDateData content typeGroupProviderType
1.0Dec 13, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARSENITE OXIDASE
B: ARSENITE OXIDASE
C: ARSENITE OXIDASE
D: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,83116
Polyers211,7024
Non-polymers4,12912
Water23,4921304
1
A: ARSENITE OXIDASE
B: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9168
Polyers105,8512
Non-polymers2,0656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6960
ΔGint (kcal/M)-87
Surface area (Å2)31110
MethodPISA
2
C: ARSENITE OXIDASE
D: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9168
Polyers105,8512
Non-polymers2,0656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7090
ΔGint (kcal/M)-91
Surface area (Å2)31310
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)96.710, 114.250, 108.980
Angle α, β, γ (deg.)90.00, 112.44, 90.00
Int Tables number4
Space group name H-MP 1 21 1

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide ARSENITE OXIDASE


Mass: 92057.500 Da / Num. of mol.: 2 / Fragment: LARGE SUBUNIT / Source: (natural) Alcaligenes faecalis (bacteria) / Genus: Alcaligenes / Strain: NCIB 8687 / References: UniProt: Q7SIF4
#2: Protein/peptide ARSENITE OXIDASE


Mass: 13793.448 Da / Num. of mol.: 2 / Fragment: RIESKE SUBUNIT / Source: (natural) Alcaligenes faecalis (bacteria) / Genus: Alcaligenes / Strain: NCIB 8687 / References: UniProt: Q7SIF3

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Non-polymers , 6 types, 1316 molecules

#3: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Formula: C20H26N10O13P2S2
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Formula: O / Oxygen
#5: Chemical ChemComp-4MO / MOLYBDENUM(IV) ION


Mass: 95.940 Da / Num. of mol.: 2 / Formula: Mo
#6: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Formula: Fe3S4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1304 / Formula: H2O / Water

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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: 2.63 / Density percent sol: 53.18 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6000, tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
115 %PEG60001reservoir
20.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 kelvins
SourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.797, 1.746, 1.742, 1.739, 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Apr 30, 1999
RadiationMonochromator: SILICON 111 / Diffraction protocol: MAD / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelength
IDWavelengthRelative weight
11.7971.0
21.7461.0
31.7421.0
41.7391.0
50.981.0
ReflectionB iso Wilson estimate: 29.3 Å2 / D resolution high: 2.03 Å / D resolution low: 48.2 Å / Number all: 131366 / Number obs: 131366 / Observed criterion sigma F: 0 / Observed criterion sigma I: 0 / Rmerge I obs: 0.059 / NetI over sigmaI: 16.4 / Redundancy: 4 % / Percent possible obs: 93.2
Reflection
*PLUS
Number measured all: 513617
Reflection shell
*PLUS
Percent possible obs: 74.9 / Rmerge I obs: 0.389 / MeanI over sigI obs: 2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
SHARPphasing
CNS1.0refinement
CCP4(TRUNCATE)data scaling
RefineMethod to determine structure: MAD / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Sigma I: 0 / Stereochemistry target values: ENGH & HUBER
Displacement parametersB iso mean: 26.6 Å2 / Aniso B11: -8.5 Å2 / Aniso B12: 0 Å2 / Aniso B13: 1.8 Å2 / Aniso B22: 0.8 Å2 / Aniso B23: 0 Å2 / Aniso B33: 7.7 Å2
Least-squares processR factor R free: 0.223 / R factor R work: 0.193 / Highest resolution: 2.03 Å / Lowest resolution: 2 Å / Number reflection R free: 6562 / Number reflection all: 131085 / Number reflection obs: 131085
Refine hist #LASTHighest resolution: 2.03 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 14735 / Nucleic acid: 0 / Ligand: 214 / Solvent: 1304 / Total: 16253
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.02

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