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- PDB-6y4a: Crystal structure of the M295I variant of Ssl1 -

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Basic information

Entry
Database: PDB / ID: 6y4a
TitleCrystal structure of the M295I 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: 1.785 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
DepositionFeb 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
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

Downloads & links

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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)107,37312
Polymers106,8013
Non-polymers5729
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-124 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.380, 104.320, 162.330
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: 35600.492 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.: 9 / Source method: isolated from a natural source / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.785→50 Å / Num. obs: 159870 / % possible obs: 99.8 % / Redundancy: 1.9 % / CC1/2: 0.996 / Net I/σ(I): 7.64
Reflection shellResolution: 1.785→1.89 Å / Num. unique obs: 25652 / CC1/2: 0.521 / % possible all: 99

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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: 1.785→48.079 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.65 / SU ML: 0.106 / Cross valid method: NONE / ESU R: 0.123 / ESU R Free: 0.122
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2276 4262 5.095 %
Rwork0.1856 --
all0.188 --
obs-83649 99.779 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.672 Å2
Baniso -1Baniso -2Baniso -3
1--2.409 Å20 Å2-0 Å2
2---0.495 Å20 Å2
3---2.904 Å2
Refinement stepCycle: LAST / Resolution: 1.785→48.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6253 0 9 641 6903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136426
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175667
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.6448721
X-RAY DIFFRACTIONr_angle_other_deg1.3651.5813098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8045804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.92821.014365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4871551
X-RAY DIFFRACTIONr_chiral_restr0.070.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021464
X-RAY DIFFRACTIONr_nbd_refined0.1980.21250
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.25558
X-RAY DIFFRACTIONr_nbtor_refined0.1640.22975
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2507
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1910.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.29
X-RAY DIFFRACTIONr_nbd_other0.1920.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.213
X-RAY DIFFRACTIONr_mcbond_it2.1252.8083225
X-RAY DIFFRACTIONr_mcbond_other2.1232.8073224
X-RAY DIFFRACTIONr_mcangle_it3.0934.1994026
X-RAY DIFFRACTIONr_mcangle_other3.0934.24027
X-RAY DIFFRACTIONr_scbond_it2.5312.9823201
X-RAY DIFFRACTIONr_scbond_other2.5312.9823202
X-RAY DIFFRACTIONr_scangle_it3.794.3774695
X-RAY DIFFRACTIONr_scangle_other3.7894.3774696
X-RAY DIFFRACTIONr_lrange_it6.17732.9347225
X-RAY DIFFRACTIONr_lrange_other6.0932.5777085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.785-1.8320.3443350.3145672X-RAY DIFFRACTION97.8339
1.832-1.8820.3122760.2845653X-RAY DIFFRACTION99.9326
1.882-1.9360.2882790.2615543X-RAY DIFFRACTION99.9828
1.936-1.9960.2833080.2285292X-RAY DIFFRACTION99.9643
1.996-2.0610.2412420.2115270X-RAY DIFFRACTION99.9819
2.061-2.1340.2322650.1955025X-RAY DIFFRACTION99.9622
2.134-2.2140.2262570.1794862X-RAY DIFFRACTION99.9414
2.214-2.3050.2352330.1834681X-RAY DIFFRACTION100
2.305-2.4070.2242710.1714479X-RAY DIFFRACTION100
2.407-2.5250.2292240.1724308X-RAY DIFFRACTION99.9779
2.525-2.6610.2262280.1694131X-RAY DIFFRACTION100
2.661-2.8220.2752240.193849X-RAY DIFFRACTION99.9755
2.822-3.0170.2581760.1883706X-RAY DIFFRACTION100
3.017-3.2590.2091930.1863412X-RAY DIFFRACTION100
3.259-3.570.21760.1723146X-RAY DIFFRACTION99.9699
3.57-3.9910.191600.162884X-RAY DIFFRACTION100
3.991-4.6080.2081440.1452544X-RAY DIFFRACTION99.9628
4.608-5.6420.1761210.1462194X-RAY DIFFRACTION100
5.642-7.9750.194950.1921716X-RAY DIFFRACTION99.9448
7.975-48.0790.266550.2271020X-RAY DIFFRACTION99.445

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