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- PDB-6yo5: Crystal structure of the M295F variant of Ssl1 -

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Basic information

Entry
Database: PDB / ID: 6yo5
TitleCrystal structure of the M295F variant of Ssl1
Components
  • ALA-HIS-ALA
  • Copper 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 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
GGG: ALA-HIS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,47622
Polymers107,2024
Non-polymers1,27418
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-269 kcal/mol
Surface area27410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.405, 104.446, 162.179
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: 35634.508 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sviceus (bacteria) / Gene: SSEG_02446 / Production host: Escherichia coli (E. coli) / References: UniProt: B5HSR1
#2: Protein/peptide ALA-HIS-ALA


Mass: 298.318 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.: 14 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
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: 1.5→50 Å / Num. obs: 268845 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 13.05
Reflection shellResolution: 1.5→1.59 Å / Num. unique obs: 42873 / CC1/2: 0.704

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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: 1.5→48.056 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.478 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1986 1457 1.05 %
Rwork0.176 --
all0.176 --
obs-138706 98.715 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.507 Å2
Baniso -1Baniso -2Baniso -3
1--1.314 Å2-0 Å2-0 Å2
2---0.762 Å20 Å2
3---2.076 Å2
Refinement stepCycle: LAST / Resolution: 1.5→48.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 34 516 6853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175694
X-RAY DIFFRACTIONr_angle_refined_deg1.751.6448816
X-RAY DIFFRACTIONr_angle_other_deg1.5091.58113158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4475808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.70221.024371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99915973
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.931551
X-RAY DIFFRACTIONr_chiral_restr0.0840.2797
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021490
X-RAY DIFFRACTIONr_nbd_refined0.2020.21231
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.25521
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23075
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.23058
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2380
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1460.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.214
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1160.29
X-RAY DIFFRACTIONr_nbd_other0.1940.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.213
X-RAY DIFFRACTIONr_mcbond_it2.2312.2573244
X-RAY DIFFRACTIONr_mcbond_other2.2232.2563243
X-RAY DIFFRACTIONr_mcangle_it3.1833.3794048
X-RAY DIFFRACTIONr_mcangle_other3.1833.3794049
X-RAY DIFFRACTIONr_scbond_it2.7622.4653252
X-RAY DIFFRACTIONr_scbond_other2.7622.4663253
X-RAY DIFFRACTIONr_scangle_it3.9213.6014768
X-RAY DIFFRACTIONr_scangle_other3.9213.6014769
X-RAY DIFFRACTIONr_lrange_it5.63126.5197150
X-RAY DIFFRACTIONr_lrange_other5.63326.5247151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.2711040.2739836X-RAY DIFFRACTION96.6268
1.539-1.5810.2291030.2459651X-RAY DIFFRACTION97.6181
1.581-1.6270.2421000.2259437X-RAY DIFFRACTION97.7753
1.627-1.6770.217980.2069197X-RAY DIFFRACTION98.121
1.677-1.7320.254950.2058951X-RAY DIFFRACTION98.3047
1.732-1.7930.267920.1898677X-RAY DIFFRACTION98.4286
1.793-1.860.206880.1778357X-RAY DIFFRACTION98.599
1.86-1.9360.23870.1678124X-RAY DIFFRACTION98.8325
1.936-2.0220.196820.1687771X-RAY DIFFRACTION99.0165
2.022-2.1210.209790.1647470X-RAY DIFFRACTION99.1463
2.121-2.2360.166760.1617162X-RAY DIFFRACTION99.3276
2.236-2.3710.172720.1576741X-RAY DIFFRACTION99.5034
2.371-2.5350.159680.1656382X-RAY DIFFRACTION99.6447
2.535-2.7380.198630.1695976X-RAY DIFFRACTION99.8347
2.738-2.9990.201580.1815511X-RAY DIFFRACTION99.8924
2.999-3.3530.206530.1844998X-RAY DIFFRACTION99.9604
3.353-3.8710.193480.1664478X-RAY DIFFRACTION100
3.871-4.7410.145400.143799X-RAY DIFFRACTION100
4.741-6.7020.246320.1712986X-RAY DIFFRACTION99.9338
6.702-48.0560.195190.231745X-RAY DIFFRACTION99.661

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