[English] 日本語
Yorodumi
- PDB-6yzy: Crystal structure of the M295V variant of Ssl1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yzy
TitleCrystal structure of the M295V 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: 2.282 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 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Copper oxidase
BBB: Copper oxidase
CCC: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,77917
Polymers106,7593
Non-polymers1,02014
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-219 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.350, 103.960, 161.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Copper oxidase


Mass: 35586.465 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.14 %
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

-
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: 2.282→48.989 Å / Num. obs: 39762 / % possible obs: 98.8 % / Redundancy: 1.9 % / CC1/2: 0.988 / Net I/σ(I): 5.6
Reflection shellResolution: 2.282→2.294 Å / Num. unique obs: 11949 / CC1/2: 0.484

-
Processing

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

4m3h


Resolution: 2.282→48.989 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.205 / SU B: 13.923 / SU ML: 0.299 / Average fsc free: 0.7842 / Average fsc work: 0.803 / Cross valid method: NONE / ESU R: 0.381 / ESU R Free: 0.272
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2847 1994 5.015 %
Rwork0.2273 37768 -
all0.23 --
obs-39762 98.643 %
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: 36.986 Å2
Baniso -1Baniso -2Baniso -3
1--4.176 Å2-0 Å2-0 Å2
2---0.98 Å20 Å2
3---5.157 Å2
Refinement stepCycle: LAST / Resolution: 2.282→48.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6271 0 30 60 6361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136490
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175702
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.6438771
X-RAY DIFFRACTIONr_angle_other_deg1.1871.58113163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1415806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.53921.008367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64615971
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg40.573153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5361551
X-RAY DIFFRACTIONr_chiral_restr0.0490.2793
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027446
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021501
X-RAY DIFFRACTIONr_nbd_refined0.20.21203
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.25483
X-RAY DIFFRACTIONr_nbtor_refined0.1610.22941
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2181
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1770.26
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.27
X-RAY DIFFRACTIONr_nbd_other0.1790.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.010.21
X-RAY DIFFRACTIONr_mcbond_it2.2423.9263233
X-RAY DIFFRACTIONr_mcbond_other2.2423.9263232
X-RAY DIFFRACTIONr_mcangle_it3.75.8794036
X-RAY DIFFRACTIONr_mcangle_other3.75.884037
X-RAY DIFFRACTIONr_scbond_it2.014.0093257
X-RAY DIFFRACTIONr_scbond_other1.9954.0013242
X-RAY DIFFRACTIONr_scangle_it3.2445.9484735
X-RAY DIFFRACTIONr_scangle_other3.2265.9364712
X-RAY DIFFRACTIONr_lrange_it5.95143.686836
X-RAY DIFFRACTIONr_lrange_other5.93943.6846833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.282-2.3410.3421460.3612633X-RAY DIFFRACTION94.1077
2.341-2.4060.3771470.3452689X-RAY DIFFRACTION100
2.406-2.4750.3261220.3452589X-RAY DIFFRACTION97.2382
2.475-2.5510.351280.3342539X-RAY DIFFRACTION98.8144
2.551-2.6350.3721310.3112456X-RAY DIFFRACTION98.7782
2.635-2.7280.3891200.3052381X-RAY DIFFRACTION98.0784
2.728-2.830.3321130.2732357X-RAY DIFFRACTION99.6772
2.83-2.9460.3121190.2452182X-RAY DIFFRACTION98.6284
2.946-3.0770.3231100.2412140X-RAY DIFFRACTION98.6409
3.077-3.2270.3081270.2192050X-RAY DIFFRACTION98.9096
3.227-3.4020.2671030.2041972X-RAY DIFFRACTION100
3.402-3.6080.2691160.191827X-RAY DIFFRACTION99.0316
3.608-3.8570.2621030.1871751X-RAY DIFFRACTION99.3037
3.857-4.1660.246850.1711637X-RAY DIFFRACTION99.3653
4.166-4.5630.199750.1521525X-RAY DIFFRACTION99.5025
4.563-5.1010.223670.1521392X-RAY DIFFRACTION99.5904
5.101-5.8890.221680.1681229X-RAY DIFFRACTION99.387
5.889-7.210.232530.2141062X-RAY DIFFRACTION99.8209
7.21-10.1870.293420.213850X-RAY DIFFRACTION99.7763
10.187-48.9890.296190.275507X-RAY DIFFRACTION98.6867

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more