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- PDB-2yxv: The deletion mutant of Multicopper Oxidase CueO -

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Basic information

Entry
Database: PDB / ID: 2yxv
TitleThe deletion mutant of Multicopper Oxidase CueO
ComponentsBlue copper oxidase cueO
KeywordsOXIDOREDUCTASE / multicopper oxidase
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 / NITRATE ION / Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsHiguchi, Y. / Komori, H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and function of the engineered multicopper oxidase CueO from Escherichia coli--deletion of the methionine-rich helical region covering the substrate-binding site
Authors: Kataoka, K. / Komori, H. / Ueki, Y. / Konno, Y. / Kamitaka, Y. / Kurose, S. / Tsujimura, S. / Higuchi, Y. / Kano, K. / Seo, D. / Sakurai, T.
History
DepositionApr 27, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 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

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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)97,8659
Polymers97,2632
Non-polymers6027
Water7,116395
1
A: Blue copper oxidase cueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9645
Polymers48,6321
Non-polymers3324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Blue copper oxidase cueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9024
Polymers48,6321
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.982, 50.947, 86.050
Angle α, β, γ (deg.)83.20, 90.83, 66.66
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Blue copper oxidase cueO / Copper efflux oxidase / Multicopper Oxidase CueO


Mass: 48631.500 Da / Num. of mol.: 2 / Mutation: P357G/H406G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (Novagen) / References: UniProt: P36649
#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-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-C2O / CU-O-CU LINKAGE / Copper(I) oxide


Mass: 143.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 16% PEG 3350, 0.16M Potassium Nitrate, 20% Glycerol, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→25.94 Å / Num. obs: 62169

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→24.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.475 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20778 3320 5.1 %RANDOM
Rwork0.17051 ---
obs0.1724 62169 92.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-1.52 Å2-0.02 Å2
2--2.11 Å2-0.35 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.81→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6768 0 14 395 7177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226963
X-RAY DIFFRACTIONr_bond_other_d0.0010.026322
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.969451
X-RAY DIFFRACTIONr_angle_other_deg0.773314748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5515882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75624.49294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.658151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.651534
X-RAY DIFFRACTIONr_chiral_restr0.0960.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021302
X-RAY DIFFRACTIONr_nbd_refined0.1940.21212
X-RAY DIFFRACTIONr_nbd_other0.180.26459
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23336
X-RAY DIFFRACTIONr_nbtor_other0.0820.24230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0690.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6431.55660
X-RAY DIFFRACTIONr_mcbond_other0.1161.51798
X-RAY DIFFRACTIONr_mcangle_it0.73827080
X-RAY DIFFRACTIONr_scbond_it1.44532914
X-RAY DIFFRACTIONr_scangle_it1.9684.52370
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.807→1.9 Å / Total num. of bins used: 2
RfactorNum. reflection% reflection
Rfree0.223 2118 -
Rwork0.178 39441 -
obs--91.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.88810.0489-0.99830.75990.25421.58340.0645-0.03250.0532-0.0077-0.03230.0112-0.1270.0083-0.0321-0.08610.0038-0.0177-0.1753-0.0014-0.13980.42650.26220.356
21.12280.17110.07030.9731-0.2641.33130.0144-0.07080.0137-0.0154-0.00560.0082-0.0079-0.1382-0.0088-0.139-0.0099-0.0039-0.0501-0.0182-0.1482-13.0439-11.5373-42.1504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA30 - 5212 - 445
2X-RAY DIFFRACTION1AC - D701 - 7031
3X-RAY DIFFRACTION2BB30 - 5172 - 441
4X-RAY DIFFRACTION2BE - F701 - 7031

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