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

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Basic information

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 / homology
Function and homology information


arsenate reductase (azurin) / arsenate reductase (azurin) activity / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / 2 iron, 2 sulfur cluster binding / intracellular membrane-bounded organelle / membrane / metal ion binding / cytoplasm
Similarity search - Function
Phosphorylase Kinase; domain 1 - #200 / Arsenite oxidase subunit AioB/Iodate reductase subunit IdrB, small subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, large subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, 3Fe-4S cluster / Rieske 3Fe-4S / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain ...Phosphorylase Kinase; domain 1 - #200 / Arsenite oxidase subunit AioB/Iodate reductase subunit IdrB, small subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, large subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, 3Fe-4S cluster / Rieske 3Fe-4S / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / 3-layer Sandwich / Barwin-like endoglucanases / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Phosphorylase Kinase; domain 1 / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MOLYBDENUM(IV) ION / FE3-S4 CLUSTER / FE2/S2 (INORGANIC) CLUSTER / Chem-MGD / OXYGEN ATOM / Arsenite oxidase subunit AioB / Arsenite oxidase subunit AioA
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.03 Å
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.
History
DepositionNov 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version 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
Polymers211,7024
Non-polymers4,12912
Water23,4921304
1
A: ARSENITE OXIDASE
B: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9168
Polymers105,8512
Non-polymers2,0656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-87 kcal/mol
Surface area31110 Å2
MethodPISA
2
C: ARSENITE OXIDASE
D: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9168
Polymers105,8512
Non-polymers2,0656
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7090 Å2
ΔGint-91 kcal/mol
Surface area31310 Å2
MethodPISA
Unit cell
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-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein ARSENITE OXIDASE


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


Mass: 13793.448 Da / Num. of mol.: 2 / Fragment: RIESKE SUBUNIT / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / 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 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#4: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


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


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#6: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#7: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 1304 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 6000, tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %PEG60001reservoir
20.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.797, 1.746, 1.742, 1.739, 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 1999
RadiationMonochromator: SILICON 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7971
21.7461
31.7421
41.7391
50.981
ReflectionResolution: 2.03→48.2 Å / Num. all: 131366 / Num. obs: 131366 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.4
Reflection
*PLUS
Num. measured all: 513617
Reflection shell
*PLUS
% possible obs: 74.9 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
SHARPphasing
CNS1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.03→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.223 6562 RANDOM
Rwork0.193 --
all-131085 -
obs-131085 -
Displacement parametersBiso mean: 26.6 Å2
Baniso -1Baniso -2Baniso -3
1--8.5 Å20 Å21.8 Å2
2--0.8 Å20 Å2
3---7.7 Å2
Refinement stepCycle: LAST / Resolution: 2.03→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14735 0 214 1304 16253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_bond_d0.02

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