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- PDB-3od3: CueO at 1.1 A resolution including residues in previously disorde... -

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Basic information

Entry
Database: PDB / ID: 3od3
TitleCueO at 1.1 A resolution including residues in previously disordered region
ComponentsBlue copper oxidase cueO
KeywordsOXIDOREDUCTASE / multicopper oxidase / cu(I) oxidase
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
COPPER (II) ION / OXYGEN ATOM / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.1 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
DepositionAug 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Sep 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_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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

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Assembly

Deposited unit
A: Blue copper oxidase cueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8788
Polymers53,4831
Non-polymers3947
Water9,548530
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.162, 90.766, 53.639
Angle α, β, γ (deg.)90.00, 102.99, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cueO, yacK, b0123, JW0119 / 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-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
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 , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.1→19 Å / Num. all: 186417 / Num. obs: 186417 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.4
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.5 / Num. unique all: 18634 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
notnecessarymodel building
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
notnecessaryphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1KV7

1kv7


Resolution: 1.1→19 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.284 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18545 9353 5 %RANDOM
Rwork0.15382 ---
obs0.15542 177031 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.09 Å2
2---0.07 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.1→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3747 0 13 530 4290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214241
X-RAY DIFFRACTIONr_bond_other_d0.0010.022833
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9575810
X-RAY DIFFRACTIONr_angle_other_deg0.88236976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5965568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77324.703185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42315718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1591520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214960
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02816
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_it2.50342672
X-RAY DIFFRACTIONr_mcbond_other1.62241076
X-RAY DIFFRACTIONr_mcangle_it3.54264359
X-RAY DIFFRACTIONr_scbond_it4.25761569
X-RAY DIFFRACTIONr_scangle_it5.84781451
X-RAY DIFFRACTIONr_rigid_bond_restr1.03217074
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 662 -
Rwork0.334 13275 -
obs--99.91 %

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