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- PDB-7f19: Structure of the G304E mutant of CueO -

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Basic information

Entry
Database: PDB / ID: 7f19
TitleStructure of the G304E mutant of CueO
ComponentsBlue copper oxidase CueO
KeywordsOXIDOREDUCTASE / multicopper oxidase
Function / homology
Function and homology information


cuproxidase / periplasmic space / oxidoreductase activity / 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 / Twin arginine translocation (Tat) signal profile. ...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 / 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 / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.773 Å
AuthorsTakata, S.T. / Kawano, T.K. / Nakata, S.N. / Takado, K.T. / Imaizumi, R.I. / Sakai, N.S. / 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 G304E mutant of CueO
Authors: Takata, S.T. / Kawano, T.K. / Nakata, S.N. / Takado, K.T. / Imaizumi, R.I. / Sakai, N.S. / Takeshita, K.T. / Yamashita, S.Y. / Sakurai, T.S. / Kataoka, K.K.
History
DepositionJun 8, 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

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Assembly

Deposited unit
A: Blue copper oxidase CueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,57611
Polymers56,6951
Non-polymers88110
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-35 kcal/mol
Surface area16680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.892, 62.287, 96.653
Angle α, β, γ (deg.)90.000, 96.153, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

21A-879-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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: 56695.055 Da / Num. of mol.: 1 / Mutation: G304E
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, 196 molecules

#2: Chemical ChemComp-C2O / CU-O-CU LINKAGE


Mass: 143.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2O
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, 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: 1.77→48.993 Å / Num. obs: 43540 / % possible obs: 97.8 % / Redundancy: 1.79 % / CC1/2: 0.97 / Rrim(I) all: 0.198 / Net I/σ(I): 3.95
Reflection shellResolution: 1.77→1.88 Å / Mean I/σ(I) obs: 0.48 / Num. unique obs: 13250 / CC1/2: 0.466 / Rrim(I) all: 1.288 / % possible all: 95.1

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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: 1.773→48.335 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.287 / WRfactor Rwork: 0.238 / SU B: 5.555 / SU ML: 0.155 / Average fsc free: 0.768 / Average fsc work: 0.7964 / Cross valid method: FREE R-VALUE / ESU R: 0.138 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2533 2225 5.11 %
Rwork0.2056 41315 -
all0.208 --
obs-43540 98.605 %
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: 43.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.362 Å2-0 Å2-0.971 Å2
2---0.171 Å2-0 Å2
3---0.018 Å2
Refinement stepCycle: LAST / Resolution: 1.773→48.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3417 0 45 186 3648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133551
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173303
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.6424818
X-RAY DIFFRACTIONr_angle_other_deg1.2351.5727683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1695444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21222.899169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05515573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3251518
X-RAY DIFFRACTIONr_chiral_restr0.0650.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
X-RAY DIFFRACTIONr_nbd_refined0.20.2628
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.23099
X-RAY DIFFRACTIONr_nbtor_refined0.1570.21621
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2201
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.212
X-RAY DIFFRACTIONr_nbd_other0.2110.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.210
X-RAY DIFFRACTIONr_mcbond_it3.4624.391779
X-RAY DIFFRACTIONr_mcbond_other3.4634.3891778
X-RAY DIFFRACTIONr_mcangle_it4.5936.5742222
X-RAY DIFFRACTIONr_mcangle_other4.5936.5752223
X-RAY DIFFRACTIONr_scbond_it3.9114.8181770
X-RAY DIFFRACTIONr_scbond_other3.914.8021762
X-RAY DIFFRACTIONr_scangle_it5.7837.0232596
X-RAY DIFFRACTIONr_scangle_other5.7887.0072588
X-RAY DIFFRACTIONr_lrange_it7.78751.6763722
X-RAY DIFFRACTIONr_lrange_other7.77651.5333694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.773-1.8190.4921460.5182835X-RAY DIFFRACTION92.291
1.819-1.8690.5511660.5032948X-RAY DIFFRACTION98.6379
1.869-1.9230.4151660.3922865X-RAY DIFFRACTION98.8262
1.923-1.9820.351570.332835X-RAY DIFFRACTION98.8437
1.982-2.0470.3071480.2922684X-RAY DIFFRACTION99.0556
2.047-2.1190.3231400.2682631X-RAY DIFFRACTION99.2478
2.119-2.1980.291310.2452570X-RAY DIFFRACTION99.1557
2.198-2.2880.31320.2332466X-RAY DIFFRACTION99.3879
2.288-2.3890.2751170.2182374X-RAY DIFFRACTION99.4014
2.389-2.5060.3191030.2312282X-RAY DIFFRACTION99.4994
2.506-2.6410.3081230.222146X-RAY DIFFRACTION99.824
2.641-2.8010.2531150.2012036X-RAY DIFFRACTION99.7681
2.801-2.9930.2441120.2071912X-RAY DIFFRACTION99.3618
2.993-3.2320.3111010.2091749X-RAY DIFFRACTION97.7801
3.232-3.5390.235980.2011607X-RAY DIFFRACTION97.3174
3.539-3.9540.259730.1821493X-RAY DIFFRACTION99.3025
3.954-4.5610.169730.1511340X-RAY DIFFRACTION99.7881
4.561-5.5740.177560.1481136X-RAY DIFFRACTION99.9162
5.574-7.8320.208430.168894X-RAY DIFFRACTION100
7.832-48.3350.239250.231511X-RAY DIFFRACTION97.8102

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