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- PDB-6im7: CueO-12.1 multicopper oxidase -

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Basic information

Entry
Database: PDB / ID: 6im7
TitleCueO-12.1 multicopper oxidase
ComponentsBlue copper oxidase CueO,12.1 peptide,Blue copper oxidase CueO
KeywordsOXIDOREDUCTASE / Multicopper oxidase / Laccase
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
Multicopper oxidase CueO
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsWongsantichon, J. / Robinson, R. / Ghadessy, F.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Development and structural characterization of an engineered multi-copper oxidase reporter of protein-protein interactions.
Authors: Sana, B. / Chee, S.M.Q. / Wongsantichon, J. / Raghavan, S. / Robinson, R.C. / Ghadessy, F.J.
History
DepositionOct 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blue copper oxidase CueO,12.1 peptide,Blue copper oxidase CueO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1662
Polymers56,1261
Non-polymers401
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-6 kcal/mol
Surface area17090 Å2
Unit cell
Length a, b, c (Å)76.111, 100.731, 59.044
Angle α, β, γ (deg.)90.000, 96.165, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-601-

CA

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Components

#1: Protein Blue copper oxidase CueO,12.1 peptide,Blue copper oxidase CueO / Copper efflux oxidase


Mass: 56126.082 Da / Num. of mol.: 1 / Mutation: M358I
Source method: isolated from a genetically manipulated source
Details: Chimera protein CueO-12.1 multicopper oxidase
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) synthetic construct (others)
Strain: K12 / Gene: cueO, yacK, b0123, JW0119 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P36649
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% w/v Polyethylene glycol 3000, 100mM TRIS pH 7, 200mM Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 31017 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 23.47 Å2 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.021 / Rrim(I) all: 0.041 / Χ2: 0.893 / Net I/σ(I): 19.7 / Num. measured all: 115207
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-23.40.20415170.9560.130.2430.90999.5
2-2.043.60.17315810.9660.1060.2040.975100
2.04-2.083.70.15414980.9770.0930.180.99999.8
2.08-2.123.70.13215610.9830.080.1550.979100
2.12-2.173.70.12415620.9860.0740.1450.9699.9
2.17-2.223.80.10815250.9880.0650.1260.963100
2.22-2.273.70.09215600.9890.0560.1080.9899.9
2.27-2.343.80.0815550.9920.0480.0930.938100
2.34-2.43.80.0715370.9940.0420.0820.894100
2.4-2.483.80.06415300.9940.0380.0750.92799.9
2.48-2.573.80.05515560.9950.0330.0640.862100
2.57-2.673.80.04815520.9960.0280.0560.888100
2.67-2.793.80.03815550.9970.0230.0440.82499.9
2.79-2.943.80.03215590.9970.0190.0370.77799.9
2.94-3.133.80.02715410.9980.0160.0320.72199.9
3.13-3.373.80.02515560.9980.0150.0290.74799.9
3.37-3.713.70.02915740.9970.0170.0341.134100
3.71-4.243.70.02915460.9970.0180.0351.38499.6
4.24-5.343.60.0215690.9980.0120.0230.64199.9
5.34-303.70.01515830.9990.0090.0170.39199.7

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KV7

1kv7


Resolution: 1.97→29.35 Å / SU ML: 0.1459 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.8578 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1844 1564 5.06 %
Rwork0.14 29369 -
obs0.1422 30933 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.78 Å2
Refinement stepCycle: LAST / Resolution: 1.97→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3541 0 1 352 3894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663663
X-RAY DIFFRACTIONf_angle_d0.85984979
X-RAY DIFFRACTIONf_chiral_restr0.0558549
X-RAY DIFFRACTIONf_plane_restr0.005653
X-RAY DIFFRACTIONf_dihedral_angle_d5.35663036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.030.17921170.14282447X-RAY DIFFRACTION90.89
2.03-2.110.20621360.15392705X-RAY DIFFRACTION99.82
2.11-2.190.22631370.15562688X-RAY DIFFRACTION100
2.19-2.290.20151520.14792661X-RAY DIFFRACTION99.96
2.29-2.410.20251360.14912688X-RAY DIFFRACTION100
2.41-2.560.19941610.15062662X-RAY DIFFRACTION100
2.56-2.760.21061520.15322689X-RAY DIFFRACTION99.96
2.76-3.040.18041450.14982691X-RAY DIFFRACTION99.89
3.04-3.480.19531230.14172729X-RAY DIFFRACTION99.93
3.48-4.380.17211510.12192674X-RAY DIFFRACTION99.79
4.38-29.350.15011540.12912735X-RAY DIFFRACTION99.59
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.313492484394-0.0009230192605240.3425257512220.151125319208-0.09273147714370.482227102016-0.0228110677665-0.0612607392438-0.04777108431260.0443857962078-0.0358555298369-0.00838745637603-0.08148625564110.0529889174312-6.98024363126E-60.1393483088650.00211573465969-0.002078033568280.1341418286570.003653519191540.13604726356121.7561950216-16.962325228876.0059681857
20.764825801004-0.1905415677440.1465124907520.251254662647-0.0697670932270.2491894317620.0262314024862-0.07423590537060.00297616685348-0.0375074094856-0.01709011485430.0505594832935-0.0599612033929-0.101773676047-7.44574495559E-50.1493760250230.01493850817720.002972342718450.131977896083-0.01253608832110.128134018619-0.0164225878683-19.383293973770.9008937166
31.101889999840.07505189861710.3381361965930.210023841202-0.01802888243650.827658144759-0.01960071761830.111470819816-0.0642700723449-0.0100744772840.00935021232149-0.0348546168649-0.04015178523520.0677754517948-2.28155347014E-50.1309546686180.008862644705210.01197909840.119424451453-0.01052201863590.13551551481713.2379153041-23.770742560759.639551476
40.47218487540.2290133279950.01422251598640.6037017688360.01593570810130.2418056274930.256243716337-0.241490641697-0.4849041129290.152048616795-0.108058840522-0.2829409579840.1801229934660.01883346907930.03437525185620.1858823613340.0530218477805-0.0365013846420.1622780386410.01007700922820.33206303678321.4787590325-36.099116783380.4122360206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 422 through 518 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 141 )
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 356 )
4X-RAY DIFFRACTION4chain 'A' and (resid 357 through 421 )

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