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- PDB-3nsd: Silver bound to the multicopper oxidase CueO (untagged) -

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Basic information

Entry
Database: PDB / ID: 3nsd
TitleSilver bound to the multicopper oxidase CueO (untagged)
ComponentsBlue copper oxidase cueO
KeywordsOXIDOREDUCTASE / multicopper oxidase / silver
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions, oxygen as acceptor / cuproxidase / oxidoreductase activity, acting on metal ions / detoxification of copper ion / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to copper ion / ferroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
SILVER ION / COPPER (II) ION / OXYGEN ATOM / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / UNnecessary / Resolution: 2 Å
AuthorsMontfort, W.R. / Roberts, S.A. / Singh, S.K.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Crystal structures of multicopper oxidase CueO bound to copper(I) and silver(I): functional role of a methionine-rich sequence.
Authors: Singh, S.K. / Roberts, S.A. / McDevitt, S.F. / Weichsel, A. / Wildner, G.F. / Grass, G.B. / Rensing, C. / Montfort, W.R.
History
DepositionJul 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_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_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_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_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_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_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: Blue copper oxidase cueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0779
Polymers53,4831
Non-polymers5948
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.181, 90.324, 53.810
Angle α, β, γ (deg.)90.00, 102.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Blue copper oxidase cueO / Copper efflux oxidase


Mass: 53483.285 Da / Num. of mol.: 1 / Fragment: UNP residues 29-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b0123, cueO, CueO (YacK), JW0119, yacK / Plasmid: pASK-IBA3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36649
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ag
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#5: 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 16% polyethylene glycol 4000, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 4.6; , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 12, 2008 / Details: osmic confocal blue
RadiationMonochromator: osmic confocal blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→26.4 Å / Num. all: 30337 / Num. obs: 30337 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / % possible all: 93

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: UNnecessary
Starting model: 1KV7

1kv7


Resolution: 2→26.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.454 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23782 1541 5.1 %RANDOM
Rwork0.18713 ---
obs0.18965 28785 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.732 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å2-0.21 Å2
2---1.2 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 8 310 3867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223646
X-RAY DIFFRACTIONr_bond_other_d0.0010.022455
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.9624957
X-RAY DIFFRACTIONr_angle_other_deg0.9336018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8625462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62124.645155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3115603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0921517
X-RAY DIFFRACTIONr_chiral_restr0.0930.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7831.52303
X-RAY DIFFRACTIONr_mcbond_other0.2071.5937
X-RAY DIFFRACTIONr_mcangle_it1.35423711
X-RAY DIFFRACTIONr_scbond_it2.3231343
X-RAY DIFFRACTIONr_scangle_it3.5854.51246
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 116 -
Rwork0.274 2066 -
obs--93.37 %

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