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- PDB-1pf3: Crystal Structure of the M441L mutant of the multicopper oxidase CueO -

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Basic information

Entry
Database: PDB / ID: 1pf3
TitleCrystal Structure of the M441L mutant of the multicopper oxidase CueO
ComponentsBlue copper oxidase cueO
KeywordsOXIDOREDUCTASE / copper / multicopper 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
CU-CL-CU LINKAGE / COPPER (II) ION / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsRoberts, S.A. / Wildner, G.F. / Grass, G. / Weichsel, A. / Ambrus, A. / Rensing, C. / Montfort, W.R.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: A Labile Regulatory Copper Ion Lies Near the T1 Copper Site in the Multicopper Oxidase CueO.
Authors: Roberts, S.A. / Wildner, G.F. / Grass, G. / Weichsel, A. / Ambrus, A. / Rensing, C. / Montfort, W.R.
History
DepositionMay 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)54,9414
Polymers54,6521
Non-polymers2903
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.445, 91.193, 53.905
Angle α, β, γ (deg.)90.00, 102.35, 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: 54651.520 Da / Num. of mol.: 1 / Mutation: M441L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CUEO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P36649
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-C2C / CU-CL-CU LINKAGE


Mass: 162.545 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: ClCu2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEG, 200 mM ammonium acetate, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 63714 / Num. obs: 63714 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rsym value: 0.066 / Net I/σ(I): 20.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7119 / Rsym value: 0.18 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.1.22refinement
CrystalClearD*TREK (MSC/RIGAKU)data scaling
RefinementStarting model: pdb entry 1KV7

1kv7


Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.227 / SU ML: 0.048
Isotropic thermal model: Isotropic, except copper, chlorine anisotropic
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The T1 copper is partially depleted (around 50% occupancy) The T2 copper is somewhat less depleted. MISSING FROM THE MODEL ARE RESIDUES 1- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The T1 copper is partially depleted (around 50% occupancy) The T2 copper is somewhat less depleted. MISSING FROM THE MODEL ARE RESIDUES 1-30 AT THE N-TERMINUS (1-28 ARE A PRESUMABLY CLEAVED SIGNAL PEPTIDE, 29-30 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP), AND RESIDUES 380-402 WHICH ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP AND, PRESUMABLY, DISORDERED. A strep tag on the C terminus has not been cleaved but is not visible in the electron density maps.
RfactorNum. reflection% reflectionSelection details
Rfree0.22757 3211 5 %from pdb entry 1KV7
Rwork0.19099 ---
obs0.19283 63714 83.74 %-
all-63714 --
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: 15.712 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3565 0 5 427 3997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213657
X-RAY DIFFRACTIONr_bond_other_d0.0020.023335
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9564970
X-RAY DIFFRACTIONr_angle_other_deg0.85137784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6785463
X-RAY DIFFRACTIONr_chiral_restr0.0970.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024073
X-RAY DIFFRACTIONr_gen_planes_other0.010.02680
X-RAY DIFFRACTIONr_nbd_refined0.2040.2589
X-RAY DIFFRACTIONr_nbd_other0.2540.23794
X-RAY DIFFRACTIONr_nbtor_other0.0850.22144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.29
X-RAY DIFFRACTIONr_mcbond_it0.9271.52308
X-RAY DIFFRACTIONr_mcangle_it1.62523721
X-RAY DIFFRACTIONr_scbond_it2.59231349
X-RAY DIFFRACTIONr_scangle_it4.0914.51249
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.206 284
Rwork0.184 5148

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