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- PDB-5b7e: Structure of perdeuterated CueO -

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Basic information

Entry
Database: PDB / ID: 5b7e
TitleStructure of perdeuterated CueO
ComponentsBlue copper oxidase CueO
KeywordsOXIDOREDUCTASE / Multicopper Oxidase / perdeuterated
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
CU-O-CU LINKAGE / COPPER (II) ION / PHOSPHATE ION / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsAkter, M. / Higuchi, Y. / Shibata, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography
Authors: Akter, M. / Inoue, C. / Komori, H. / Matsuda, N. / Sakurai, T. / Kataoka, K. / Higuchi, Y. / Shibata, N.
History
DepositionJun 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Derived calculations / Experimental preparation
Category: diffrn_source / exptl_crystal_grow / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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)58,2816
Polymers57,8231
Non-polymers4575
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-34 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.321, 70.416, 134.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 57823.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: cueO / Production host: Escherichia coli (E. coli) / References: UniProt: P36649

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Non-polymers , 5 types, 562 molecules

#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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 14 % (w/v) PEG 8000, 0.1 M Na HEPES, pD 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 94351 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.052 / Net I/σ(I): 31.4
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 1.76 / CC1/2: 0.709 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IKV7

Resolution: 1.42→31.2 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.42
RfactorNum. reflection% reflection
Rfree0.1827 2000 2.12 %
Rwork0.1564 --
obs0.157 94347 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.42→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 15 558 4241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073832
X-RAY DIFFRACTIONf_angle_d1.1485192
X-RAY DIFFRACTIONf_dihedral_angle_d12.2981419
X-RAY DIFFRACTIONf_chiral_restr0.075568
X-RAY DIFFRACTIONf_plane_restr0.005678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4179-1.45340.26541370.24166356X-RAY DIFFRACTION98
1.4534-1.49270.2751420.22146526X-RAY DIFFRACTION100
1.4927-1.53660.19851420.20256536X-RAY DIFFRACTION100
1.5366-1.58620.2631410.18616543X-RAY DIFFRACTION100
1.5862-1.64290.20591410.17476515X-RAY DIFFRACTION100
1.6429-1.70860.2051420.16296564X-RAY DIFFRACTION100
1.7086-1.78640.16781430.15896575X-RAY DIFFRACTION100
1.7864-1.88060.19861420.16036562X-RAY DIFFRACTION100
1.8806-1.99840.16151430.15566609X-RAY DIFFRACTION100
1.9984-2.15260.17241430.14826580X-RAY DIFFRACTION100
2.1526-2.36920.18821440.15076652X-RAY DIFFRACTION100
2.3692-2.71180.16221440.16066646X-RAY DIFFRACTION100
2.7118-3.4160.19681450.14946727X-RAY DIFFRACTION100
3.416-31.17560.15951510.14066956X-RAY DIFFRACTION100

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