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- PDB-3nt0: C500S (T1D) Mutant of CueO soaked in and bound to Cu(I) -

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Basic information

Entry
Database: PDB / ID: 3nt0
TitleC500S (T1D) Mutant of CueO soaked in and bound to Cu(I)
ComponentsBlue copper oxidase cueO
KeywordsOXIDOREDUCTASE / multicopper oxidase / copper(I) / C500S mutant
Function / homology
Function and homology information


cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor / 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 / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / 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
ACETATE ION / COPPER (I) ION / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / UNnecessary / Resolution: 1.8 Å
AuthorsRoberts, S.A. / Montfort, W.R. / 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 2, 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_ref_seq_dif / 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.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_ref_seq_dif.details / _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)56,02011
Polymers55,3891
Non-polymers63110
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.861, 92.507, 54.330
Angle α, β, γ (deg.)90.00, 102.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Blue copper oxidase cueO


Mass: 55389.301 Da / Num. of mol.: 1 / Mutation: C500S
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-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.25 Å3/Da / Density % sol: 45.41 %
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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2004
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.8→20.5 Å / Num. all: 45480 / Num. obs: 42528 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4405 / % possible all: 93

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Processing

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

1kv7


Resolution: 1.8→20.5 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.88 / SU B: 2.762 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26082 2159 5.1 %RANDOM
Rwork0.20663 ---
obs0.20937 40340 93.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.608 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0.86 Å2
2---0.56 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 13 386 3994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223805
X-RAY DIFFRACTIONr_bond_other_d0.0010.022548
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.9635185
X-RAY DIFFRACTIONr_angle_other_deg1.16636267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66924.658161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4415640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2781518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
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_it0.7971.52403
X-RAY DIFFRACTIONr_mcbond_other0.1931.5973
X-RAY DIFFRACTIONr_mcangle_it1.42623888
X-RAY DIFFRACTIONr_scbond_it2.21231402
X-RAY DIFFRACTIONr_scangle_it3.5754.51296
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 168 -
Rwork0.272 3032 -
obs--95.69 %

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