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- PDB-1g8k: CRYSTAL STRUCTURE ANALYSIS OF ARSENITE OXIDASE FROM ALCALIGENES F... -

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Basic information

Entry
Database: PDB / ID: 1g8k
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 / oxidoreductase complex / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / NADH dehydrogenase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / metal ion binding / membrane
Similarity search - Function
Immunoglobulin-like - #4210 / 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 / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin dinucleotide-binding domain ...Immunoglobulin-like - #4210 / 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 / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Barwin-like endoglucanases - #20 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Barwin-like endoglucanases / Rieske iron-sulphur protein, C-terminal / Rieske iron-sulphur protein / Aspartate decarboxylase-like domain superfamily / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / : / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Phosphorylase Kinase; domain 1 / Beta Barrel / Immunoglobulin-like / Sandwich / 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 / MOLECULAR REPLACEMENT / Resolution: 1.64 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 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 5, 2011Group: Other
Revision 1.4Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.5Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ARSENITE OXIDASE
B: ARSENITE OXIDASE
C: ARSENITE OXIDASE
D: ARSENITE OXIDASE
E: ARSENITE OXIDASE
F: ARSENITE OXIDASE
G: ARSENITE OXIDASE
H: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)435,21461
Polymers423,6698
Non-polymers11,54553
Water73,6274087
1
A: ARSENITE OXIDASE
B: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,78815
Polymers105,9172
Non-polymers2,87113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-155 kcal/mol
Surface area31680 Å2
MethodPISA, PQS
2
C: ARSENITE OXIDASE
D: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,78815
Polymers105,9172
Non-polymers2,87113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-154 kcal/mol
Surface area31670 Å2
MethodPISA, PQS
3
E: ARSENITE OXIDASE
F: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,85016
Polymers105,9172
Non-polymers2,93314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-152 kcal/mol
Surface area31720 Å2
MethodPISA, PQS
4
G: ARSENITE OXIDASE
H: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,78815
Polymers105,9172
Non-polymers2,87113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-154 kcal/mol
Surface area31820 Å2
MethodPISA, PQS
5
E: ARSENITE OXIDASE
F: ARSENITE OXIDASE
G: ARSENITE OXIDASE
H: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,63831
Polymers211,8344
Non-polymers5,80427
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22630 Å2
ΔGint-327 kcal/mol
Surface area57270 Å2
MethodPISA
6
A: ARSENITE OXIDASE
B: ARSENITE OXIDASE
C: ARSENITE OXIDASE
D: ARSENITE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,57630
Polymers211,8344
Non-polymers5,74126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22380 Å2
ΔGint-331 kcal/mol
Surface area57180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.740, 109.520, 117.640
Angle α, β, γ (deg.)97.71, 90.00, 96.43
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
ARSENITE OXIDASE


Mass: 92111.656 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: NCIB 8687 / References: UniProt: Q7SIF4
#2: Protein
ARSENITE OXIDASE


Mass: 13805.501 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alcaligenes faecalis (bacteria) / Strain: NCIB 8687 / References: UniProt: Q7SIF3

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Non-polymers , 9 types, 4140 molecules

#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Hg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: 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.: 8 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical
ChemComp-O / OXYGEN ATOM


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


Mass: 95.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mo
#8: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4087 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 10000, cobalt(II) chloride, calcium chloride, MES, mercury(II) chloride, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %PEG175001reservoir
20.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 22, 1998
RadiationMonochromator: SILICON 311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.64→17.8 Å / Num. all: 507315 / Num. obs: 507315 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.6
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 2.9 / Num. unique all: 28938 / % possible all: 71.5
Reflection
*PLUS
Num. measured all: 930124
Reflection shell
*PLUS
% possible obs: 71.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
CNS1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→17.8 Å / Isotropic thermal model: ISOTROPIC / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.179 25514 RANDOM
Rwork0.154 --
all-507315 -
obs-507315 -
Displacement parametersBiso mean: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å2-0.2 Å2-0.9 Å2
2--1.5 Å20.7 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.64→17.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29680 0 484 4087 34251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.03
X-RAY DIFFRACTIONc_angle_deg2.6
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 481801
Solvent computation
*PLUS
Displacement parameters
*PLUS

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