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- PDB-7f0v: Structure of the M305I mutant of CueO -

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Basic information

Entry
Database: PDB / ID: 7f0v
TitleStructure of the M305I mutant of CueO
ComponentsBlue copper oxidase CueO
KeywordsOXIDOREDUCTASE / multicopper oxidase
Function / homology
Function and homology information


oxidoreductase activity / 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 / Twin arginine translocation (Tat) signal profile. ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
CU-O-CU LINKAGE / COPPER (II) ION / NITRATE ION / DI(HYDROXYETHYL)ETHER / Blue copper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.494 Å
AuthorsKawano, T.K. / Takata, S.T. / Sakai, N.S. / Imaizumi, R.I. / Nakata, S.N. / Takeshita, K.T. / Yamashita, S.Y. / Sakurai, T.S. / Kataoka, K.K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K05432 Japan
Japan Agency for Medical Research and Development (AMED)BINDS1842 Japan
CitationJournal: To Be Published
Title: Structure of the M305I mutant of CueO
Authors: Kawano, T.K. / Takata, S.T. / Sakai, N.S. / Imaizumi, R.I. / Nakata, S.N. / Takeshita, K.T. / Yamashita, S.Y. / Sakurai, T.S. / Kataoka, K.K.
History
DepositionJun 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blue copper oxidase CueO
B: Blue copper oxidase CueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,23713
Polymers113,2102
Non-polymers1,02711
Water10,287571
1
A: Blue copper oxidase CueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0876
Polymers56,6051
Non-polymers4825
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-34 kcal/mol
Surface area17840 Å2
MethodPISA
2
B: Blue copper oxidase CueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1497
Polymers56,6051
Non-polymers5446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-32 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.798, 49.922, 95.933
Angle α, β, γ (deg.)86.979, 80.626, 70.535
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Blue copper oxidase CueO / Copper efflux oxidase / Copper oxidase / CueO protein / Multicopper oxidase / Multicopper oxidase ...Copper efflux oxidase / Copper oxidase / CueO protein / Multicopper oxidase / Multicopper oxidase (Laccase) / Multicopper oxidase CueO


Mass: 56604.953 Da / Num. of mol.: 2 / Mutation: M305I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: cueO, A9R57_04170, AUQ13_07730, BANRA_00502, BANRA_02318, BANRA_03294, BHS87_00550, BJJ90_21590, BMA87_12960, BUE81_03880, BvCms2454_01631, BvCmsHHP056_04875, BvCmsKKP036_02792, BvCmsKSP026_ ...Gene: cueO, A9R57_04170, AUQ13_07730, BANRA_00502, BANRA_02318, BANRA_03294, BHS87_00550, BJJ90_21590, BMA87_12960, BUE81_03880, BvCms2454_01631, BvCmsHHP056_04875, BvCmsKKP036_02792, BvCmsKSP026_04756, BvCmsSINP011_00803, BW690_21865, C5F72_22005, C5F73_07705, C5N07_08325, C6669_04510, C9E25_07140, CA593_03120, CG692_01085, CI693_14840, CWS33_09370, D0X26_09670, D3821_05970, D6T60_04275, D9C99_10035, D9D44_07015, D9I18_13120, D9J11_09660, D9J52_04795, D9Z28_05630, DAH34_04440, DJ503_00645, DNC98_11530, DT034_05590, E2119_07645, E2134_11740, E2135_03380, E4K53_07200, E4K55_07200, E4K61_10655, E5P28_13255, E5S44_09260, EA213_09430, EAI42_26240, EAI46_26365, EAI52_02170, EC1094V2_3732, EC3234A_2c01050, ECTO6_03944, EEP23_00405, EG808_12120, EI021_04575, EI041_03395, EJC75_22495, EL75_3641, EL79_3751, EL80_3698, EPT01_02830, ERS150873_01065, ETECE1441_03949, EYD11_18775, EYV18_05255, EYY78_13140, FRV13_02155, FV293_03130, G5632_10235, G5688_04010, G5696_01080, G9P49_18255, GHD50_13365, GKF39_00960, GKF74_00135, GKF86_00960, GKF89_02255, GKG12_02350, GQE22_02395, GQE33_14025, GQE34_09055, GQE42_19525, GQE64_01625, GQM04_26830, GRW02_08355, GRW05_24815, GRW57_18925, GRW80_09165, GRW81_09580, H4P50_20865, H4P51_20715, HH707_001039, HLT96_06715, HLU13_04335, HMQ05_02945, HNC40_15140, HNC94_15135, HNN86_16410, HPE39_04120, HV005_17560, HV022_19655, HV068_19765, HV109_19610, HVX22_18960, HVY77_21410, HVY79_03855, HVY93_19425, HVZ24_18700, HVZ62_10495, HX136_20845, NCTC11022_04845, NCTC9045_04770, NCTC9058_02748, NCTC9062_04168, NCTC9706_01385, RK56_013325, SAMEA3472043_02481, SAMEA3472070_02440, SAMEA3484427_01313, SAMEA3484429_01168, SAMEA3752557_00827, SAMEA3752559_03758, SAMEA3753300_01926, SK85_00121, WP2S18E08_38200, WP7S17E04_36210, WQ89_09325
Production host: Escherichia coli (E. coli) / References: UniProt: W8T2X0, Oxidoreductases

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Non-polymers , 5 types, 582 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-C2O / CU-O-CU LINKAGE / Copper(I) oxide


Mass: 143.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2O
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.96 Å3/Da / Density % sol: 37.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, KNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.494→47.371 Å / Num. obs: 132574 / % possible obs: 92.8 % / Redundancy: 8.7 % / CC1/2: 0.991 / Net I/σ(I): 5.63
Reflection shellResolution: 1.494→1.58 Å / Num. unique obs: 42045 / Rrim(I) all: 1.065 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3od3

3od3


Resolution: 1.494→47.371 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.94 / SU ML: 0.098 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2322 6644 5.012 %
Rwork0.1872 125930 -
all0.189 --
obs-132574 95.127 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 37.442 Å2
Baniso -1Baniso -2Baniso -3
1-1.009 Å2-1.395 Å20.062 Å2
2--0.558 Å20.355 Å2
3----2.574 Å2
Refinement stepCycle: LAST / Resolution: 1.494→47.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7288 0 42 571 7901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137573
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177033
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.63910278
X-RAY DIFFRACTIONr_angle_other_deg1.311.57216379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.785960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60123.155355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.415151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.481535
X-RAY DIFFRACTIONr_chiral_restr0.0720.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021463
X-RAY DIFFRACTIONr_nbd_refined0.2080.21370
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.26523
X-RAY DIFFRACTIONr_nbtor_refined0.1570.23482
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23420
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2432
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0840.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.223
X-RAY DIFFRACTIONr_nbd_other0.1970.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.216
X-RAY DIFFRACTIONr_mcbond_it3.0673.7873831
X-RAY DIFFRACTIONr_mcbond_other3.0673.7873830
X-RAY DIFFRACTIONr_mcangle_it4.0495.6754794
X-RAY DIFFRACTIONr_mcangle_other4.0495.6754795
X-RAY DIFFRACTIONr_scbond_it3.7474.1413742
X-RAY DIFFRACTIONr_scbond_other3.7464.1413743
X-RAY DIFFRACTIONr_scangle_it5.2886.0395484
X-RAY DIFFRACTIONr_scangle_other5.2876.0395485
X-RAY DIFFRACTIONr_lrange_it6.81445.3558042
X-RAY DIFFRACTIONr_lrange_other6.80845.0587947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.494-1.5330.4584680.4369090X-RAY DIFFRACTION92.5804
1.533-1.5750.4144760.3888993X-RAY DIFFRACTION94.586
1.575-1.620.3424770.3568813X-RAY DIFFRACTION94.7283
1.62-1.670.3084170.3118614X-RAY DIFFRACTION95.0231
1.67-1.7250.3244570.2818249X-RAY DIFFRACTION94.754
1.725-1.7860.284600.2498100X-RAY DIFFRACTION95.8137
1.786-1.8530.2654120.2327848X-RAY DIFFRACTION95.9795
1.853-1.9290.283970.2277509X-RAY DIFFRACTION96.2972
1.929-2.0140.2533770.2147262X-RAY DIFFRACTION96.6473
2.014-2.1130.2893790.2156915X-RAY DIFFRACTION96.5837
2.113-2.2270.2463400.2026626X-RAY DIFFRACTION96.4152
2.227-2.3620.2463360.1896209X-RAY DIFFRACTION96.0522
2.362-2.5250.2432920.1785818X-RAY DIFFRACTION95.4688
2.525-2.7270.2382590.1835375X-RAY DIFFRACTION94.2613
2.727-2.9870.2442570.1714928X-RAY DIFFRACTION94.8939
2.987-3.3390.2082090.1674484X-RAY DIFFRACTION94.5026
3.339-3.8550.2092300.1623895X-RAY DIFFRACTION94.372
3.855-4.7190.1761740.1363235X-RAY DIFFRACTION93.3717
4.719-6.6660.1771430.1522589X-RAY DIFFRACTION95.3578
6.666-47.3710.235840.1931378X-RAY DIFFRACTION92.7665

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