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- PDB-6yzd: Crystal structure of the M295A variant of Ssl1 -

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Basic information

Entry
Database: PDB / ID: 6yzd
TitleCrystal structure of the M295A variant of Ssl1
ComponentsCopper oxidase
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,75719
Polymers106,6753
Non-polymers1,08216
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-217 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.440, 104.100, 163.130
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: 35558.414 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: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.05 Å3/Da / Density % sol: 39.92 %
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: May 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→30.36 Å / Num. obs: 168970 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 13
Reflection shellResolution: 1.41→1.43 Å / Num. unique obs: 8312 / CC1/2: 0.621

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M3H

4m3h


Resolution: 1.41→30.36 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.785 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.063 / ESU R Free: 0.065
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2249 8343 4.938 %
Rwork0.1998 --
all0.201 --
obs-168969 99.828 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.936 Å2
Baniso -1Baniso -2Baniso -3
1--1.758 Å2-0 Å2-0 Å2
2---0.835 Å20 Å2
3---2.593 Å2
Refinement stepCycle: LAST / Resolution: 1.41→30.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6286 0 24 255 6565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136478
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175690
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.6458794
X-RAY DIFFRACTIONr_angle_other_deg1.4821.5813151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3855810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.61120.997371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42515975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7741552
X-RAY DIFFRACTIONr_chiral_restr0.0760.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021483
X-RAY DIFFRACTIONr_nbd_refined0.1970.21130
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.25253
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23049
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22949
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0590.22
X-RAY DIFFRACTIONr_metal_ion_refined0.070.219
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.24
X-RAY DIFFRACTIONr_nbd_other0.1870.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.23
X-RAY DIFFRACTIONr_mcbond_it1.8992.2123243
X-RAY DIFFRACTIONr_mcbond_other1.8942.2113242
X-RAY DIFFRACTIONr_mcangle_it2.5953.3134049
X-RAY DIFFRACTIONr_mcangle_other2.5953.3144050
X-RAY DIFFRACTIONr_scbond_it2.4142.4173235
X-RAY DIFFRACTIONr_scbond_other2.4012.4143228
X-RAY DIFFRACTIONr_scangle_it3.5473.5294744
X-RAY DIFFRACTIONr_scangle_other3.5243.5234733
X-RAY DIFFRACTIONr_lrange_it4.58525.1016902
X-RAY DIFFRACTIONr_lrange_other4.58425.0456862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.4470.3426220.32711744X-RAY DIFFRACTION99.7419
1.447-1.4860.316280.31111421X-RAY DIFFRACTION99.8591
1.486-1.5290.3115530.28811177X-RAY DIFFRACTION99.7449
1.529-1.5760.2895540.26610857X-RAY DIFFRACTION99.8338
1.576-1.6280.2475490.24410485X-RAY DIFFRACTION99.81
1.628-1.6850.2555020.22710211X-RAY DIFFRACTION99.8881
1.685-1.7490.2335370.2129790X-RAY DIFFRACTION99.9129
1.749-1.820.2375350.1989430X-RAY DIFFRACTION99.8397
1.82-1.9010.2334610.1899155X-RAY DIFFRACTION99.8339
1.901-1.9940.2234320.198693X-RAY DIFFRACTION99.9343
1.994-2.1020.2094400.1898266X-RAY DIFFRACTION99.8738
2.102-2.2290.2264320.1857863X-RAY DIFFRACTION99.9398
2.229-2.3830.2363830.1887409X-RAY DIFFRACTION99.9743
2.383-2.5740.2163370.1886951X-RAY DIFFRACTION99.9863
2.574-2.820.2353270.1996377X-RAY DIFFRACTION100
2.82-3.1520.2282910.2095803X-RAY DIFFRACTION99.9508
3.152-3.640.2172700.1965161X-RAY DIFFRACTION99.8896
3.64-4.4570.1672080.1574384X-RAY DIFFRACTION100
4.457-6.3010.1821860.1663454X-RAY DIFFRACTION99.9451
6.301-30.360.245960.2241995X-RAY DIFFRACTION98.5391

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