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- PDB-1kv7: Crystal Structure of CueO, a multi-copper oxidase from E. coli in... -

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Basic information

Entry
Database: PDB / ID: 1kv7
TitleCrystal Structure of CueO, a multi-copper oxidase from E. coli involved in copper homeostasis
ComponentsPROBABLE BLUE-COPPER PROTEIN YACK
KeywordsOXIDOREDUCTASE / multi-copper oxidase / T1 (blue) copper
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-O-CU LINKAGE / COPPER (II) ION / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsRoberts, S.A. / Weichsel, A. / Grass, G. / Thakali, K. / Hazzard, J.T. / Tollin, G. / Rensing, C. / Montfort, W.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure and electron transfer kinetics of CueO, a multicopper oxidase required for copper homeostasis in Escherichia coli.
Authors: Roberts, S.A. / Weichsel, A. / Grass, G. / Thakali, K. / Hazzard, J.T. / Tollin, G. / Rensing, C. / Montfort, W.R.
History
DepositionJan 25, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: PROBABLE BLUE-COPPER PROTEIN YACK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7534
Polymers53,4831
Non-polymers2703
Water9,134507
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.820, 90.510, 53.090
Angle α, β, γ (deg.)90.00, 102.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROBABLE BLUE-COPPER PROTEIN YACK / CueO


Mass: 53483.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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-C2O / CU-O-CU LINKAGE


Mass: 143.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 298 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 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG40001reservoir
2200 mMammonium acetate1reservoir
3100 mMsodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.000, 1.3772, 1.1922, 1.3804
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.37721
31.19221
41.38041
ReflectionResolution: 1.4→26 Å / Num. all: 88158 / Num. obs: 88158 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.064 / Net I/σ(I): 7
Reflection shellResolution: 1.4→1.49 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.28 / % possible all: 87
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. obs: 88826 / % possible obs: 98.5 % / Num. measured all: 733346 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 87.1 % / Rmerge(I) obs: 0.28

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Processing

Software
NameClassification
MLPHAREphasing
DMmodel building
SHELXL-97refinement
Blu-Icedata collection
d*TREKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→26 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: 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 ...Details: 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.
RfactorNum. reflectionSelection details
Rfree0.221 4483 random
Rwork0.185 --
all-88139 -
obs-88139 -
Refinement stepCycle: LAST / Resolution: 1.4→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 5 507 4073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.026
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor all: 0.19 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.026

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