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- PDB-6yzf: Crystal structure of the M295Y variant of Ssl1 -

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Basic information

Entry
Database: PDB / ID: 6yzf
TitleCrystal structure of the M295Y variant of Ssl1
Components
  • Copper oxidase
  • GLU-HIS-SER
KeywordsOXIDOREDUCTASE / Laccase / Ssl1 / Cu-binding protein
Function / homology
Function and homology information


iron ion transport / oxidoreductase activity / copper ion binding / plasma membrane
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / 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
COPPER (II) ION / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces sviceus ATCC 29083 (bacteria)
Streptomyces sviceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.684 Å
AuthorsMielenbrink, S. / Olbrich, A. / Urlacher, V. / Span, I.
CitationJournal: Chemistry / Year: 2024
Title: Substitution of the axial Type 1 Cu Ligand Afford Binding of a Water Molecule in Axial Position Affecting Kinetics, Spectral, and Structural Properties of the Small Laccase Ssl1.
Authors: Olbrich, A.C. / Mielenbrink, S. / Willers, V.P. / Koschorreck, K. / Birrell, J.A. / Span, I. / Urlacher, V.B.
History
DepositionMay 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Copper oxidase
BBB: Copper oxidase
CCC: Copper oxidase
FFF: GLU-HIS-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,24817
Polymers107,3244
Non-polymers92413
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-217 kcal/mol
Surface area27040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.400, 104.240, 162.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Copper oxidase


Mass: 35650.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sviceus ATCC 29083 (bacteria)
Gene: SSEG_02446 / Production host: Escherichia coli (E. coli) / References: UniProt: B5HSR1
#2: Protein/peptide GLU-HIS-SER


Mass: 372.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Part of the protein chain, but position is unknown / Source: (gene. exp.) Streptomyces sviceus (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50 mM HEPES pH 7.0, 1.4 M ammonium sulfate, 10 mM [Co(NH3)6]Cl3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→49.043 Å / Num. obs: 98807 / % possible obs: 99.3 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 8.87
Reflection shellResolution: 1.684→1.692 Å / Num. unique obs: 4562 / CC1/2: 0.572

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M3H

4m3h


Resolution: 1.684→49.043 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.182 / SU B: 3.077 / SU ML: 0.094 / Average fsc free: 0.8674 / Average fsc work: 0.8793 / Cross valid method: NONE / ESU R: 0.106 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.232 4943 5.007 %
Rwork0.1906 93769 -
all0.193 --
obs-98712 99.271 %
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: 25.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.875 Å20 Å2-0 Å2
2--0.048 Å2-0 Å2
3---1.826 Å2
Refinement stepCycle: LAST / Resolution: 1.684→49.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6250 0 25 632 6907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136461
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175680
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.6468727
X-RAY DIFFRACTIONr_angle_other_deg1.4021.58213113
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5615795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.80621.03369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39315969
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg35.009153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1781551
X-RAY DIFFRACTIONr_chiral_restr0.0780.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027383
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021498
X-RAY DIFFRACTIONr_nbd_refined0.1950.21215
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.25583
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23003
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2514
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2260.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.211
X-RAY DIFFRACTIONr_nbd_other0.1860.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0270.21
X-RAY DIFFRACTIONr_mcbond_it2.2722.5223201
X-RAY DIFFRACTIONr_mcbond_other2.2722.5213200
X-RAY DIFFRACTIONr_mcangle_it3.3833.7663989
X-RAY DIFFRACTIONr_mcangle_other3.3833.7673990
X-RAY DIFFRACTIONr_scbond_it2.9522.7693260
X-RAY DIFFRACTIONr_scbond_other2.9022.7633248
X-RAY DIFFRACTIONr_scangle_it4.0974.054738
X-RAY DIFFRACTIONr_scangle_other4.0644.0424721
X-RAY DIFFRACTIONr_lrange_it6.1529.8177193
X-RAY DIFFRACTIONr_lrange_other6.14929.8237194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.684-1.7280.353420.3656575X-RAY DIFFRACTION95.5651
1.728-1.7750.3423620.3336669X-RAY DIFFRACTION98.7223
1.775-1.8260.3313470.296493X-RAY DIFFRACTION99.5923
1.826-1.8830.333320.2646299X-RAY DIFFRACTION99.2071
1.883-1.9440.2743200.2426108X-RAY DIFFRACTION99.1669
1.944-2.0130.2743270.2275926X-RAY DIFFRACTION99.2855
2.013-2.0890.2542910.2075772X-RAY DIFFRACTION99.475
2.089-2.1740.2442890.195520X-RAY DIFFRACTION99.6056
2.174-2.270.2392670.1925350X-RAY DIFFRACTION99.716
2.27-2.3810.2472740.1895108X-RAY DIFFRACTION99.796
2.381-2.510.2442860.1864820X-RAY DIFFRACTION99.8826
2.51-2.6620.2352600.1824627X-RAY DIFFRACTION99.9182
2.662-2.8460.2311840.1724399X-RAY DIFFRACTION99.9782
2.846-3.0740.2192230.184054X-RAY DIFFRACTION100
3.074-3.3670.2232030.1833743X-RAY DIFFRACTION100
3.367-3.7640.1931750.1613423X-RAY DIFFRACTION99.9722
3.764-4.3460.1771470.1383057X-RAY DIFFRACTION100
4.346-5.3220.1531460.1322576X-RAY DIFFRACTION100
5.322-7.5230.2331090.22043X-RAY DIFFRACTION99.9536
7.523-49.0430.254590.2131207X-RAY DIFFRACTION99.6066

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