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- PDB-6vow: Crystal structure of multi-copper oxidase from Pseudomonas Thermo... -

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Basic information

Entry
Database: PDB / ID: 6vow
TitleCrystal structure of multi-copper oxidase from Pseudomonas Thermotolerans
Componentsmulticopper oxidase
KeywordsOXIDOREDUCTASE / LACCASE / COPPER OXIDASE / ACOUSTIC DROPLET EJECTION / LIGNIN
Function / homologyCU-O-CU LINKAGE / COPPER (II) ION
Function and homology information
Biological speciesPseudomonas thermotolerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsColer, E.A. / Soares, A.S. / Collins, R.E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM111244 United States
Department of Energy (DOE, United States)KP1605010 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R21GM129570-01 United States
CitationJournal: To Be Published
Title: Crystal structure of multi-copper oxidase from Pseudomonas Thermotolerans
Authors: Coler, E.A. / Soares, A.S. / Collins, R.E.
History
DepositionJan 31, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0904
Polymers50,8201
Non-polymers2703
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.110, 68.840, 49.520
Angle α, β, γ (deg.)90.00, 93.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein multicopper oxidase


Mass: 50819.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas thermotolerans (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-C2O / CU-O-CU LINKAGE


Mass: 143.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: Crystallized in plastic sitting drop trays, 30 nl of protein (concentration 10 mg/mL) combined with 30 nl precipitant: 0.10 M Ammonium acetate 10 %(w/v) PEG 3350 Solution was equilibrated ...Details: Crystallized in plastic sitting drop trays, 30 nl of protein (concentration 10 mg/mL) combined with 30 nl precipitant: 0.10 M Ammonium acetate 10 %(w/v) PEG 3350 Solution was equilibrated against a reservoir of 60% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 31326 / % possible obs: 90.2 % / Redundancy: 19.36 % / CC1/2: 0.958 / Rmerge(I) obs: 0.42 / Net I/σ(I): 7.17
Reflection shellResolution: 1.92→1.97 Å / Rmerge(I) obs: 0.502 / Num. unique obs: 1659 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f7k

4f7k


Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 11.056 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23164 1590 5.1 %RANDOM
Rwork0.16294 ---
obs0.16632 29668 89.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20.86 Å2
2---0.08 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 5 136 3368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0193389
X-RAY DIFFRACTIONr_bond_other_d0.0030.023189
X-RAY DIFFRACTIONr_angle_refined_deg2.4081.9574612
X-RAY DIFFRACTIONr_angle_other_deg1.15437321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0315416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81422.595158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07315522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6981532
X-RAY DIFFRACTIONr_chiral_restr0.1240.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213841
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02803
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.2464.9591658
X-RAY DIFFRACTIONr_mcbond_other8.2355.1841657
X-RAY DIFFRACTIONr_mcangle_it9.4157.4352076
X-RAY DIFFRACTIONr_mcangle_other9.41629.7512077
X-RAY DIFFRACTIONr_scbond_it10.4015.4961730
X-RAY DIFFRACTIONr_scbond_other10.4035.4971729
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.2688.0532536
X-RAY DIFFRACTIONr_long_range_B_refined10.6941.233879
X-RAY DIFFRACTIONr_long_range_B_other10.65441.1363848
X-RAY DIFFRACTIONr_rigid_bond_restr4.84836575
X-RAY DIFFRACTIONr_sphericity_free34.087543
X-RAY DIFFRACTIONr_sphericity_bonded20.34156564
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 74 -
Rwork0.33 1577 -
obs--63.87 %

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