[English] 日本語
Yorodumi
- PDB-7pen: Crystal Structure of Two-Domain Laccase mutant Y230A from Strepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pen
TitleCrystal Structure of Two-Domain Laccase mutant Y230A from Streptomyces griseoflavus
ComponentsTwo-domain laccase
KeywordsOXIDOREDUCTASE / Two-Domain Laccase / laccase / Streptomyces griseoflavus
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / 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 / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGabdulkhakov, A. / Tishchenko, S. / Kolyadenko, I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-34-90121 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2021
Title: Engineering the Catalytic Properties of Two-Domain Laccase from Streptomyces griseoflavus Ac-993.
Authors: Kolyadenko, I. / Scherbakova, A. / Kovalev, K. / Gabdulkhakov, A. / Tishchenko, S.
History
DepositionAug 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,52832
Polymers207,9576
Non-polymers1,57126
Water24,1221339
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,76416
Polymers103,9793
Non-polymers78613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-155 kcal/mol
Surface area28260 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,76416
Polymers103,9793
Non-polymers78613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11380 Å2
ΔGint-155 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.260, 94.980, 116.270
Angle α, β, γ (deg.)90.000, 91.667, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
Two-domain laccase


Mass: 34659.543 Da / Num. of mol.: 6 / Mutation: Y230A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase
#2: Chemical...
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15 % v/v PEG Smear High, 0.15 M Ammonium acetate, 0.1 M Sodium citrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 220573 / % possible obs: 99.9 % / Redundancy: 5.63 % / Biso Wilson estimate: 20.11 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.1 / Net I/σ(I): 10.93
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 16337 / CC1/2: 0.68 / Rrim(I) all: 1.13 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LHL

5lhl


Resolution: 1.6→47.1 Å / SU ML: 0.1986 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.3746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1653 8823 4 %
Rwork0.1353 211735 -
obs0.1365 220558 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12750 0 26 1339 14115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006213414
X-RAY DIFFRACTIONf_angle_d0.888418257
X-RAY DIFFRACTIONf_chiral_restr0.06051863
X-RAY DIFFRACTIONf_plane_restr0.00762465
X-RAY DIFFRACTIONf_dihedral_angle_d14.34554820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.33622930.30447050X-RAY DIFFRACTION99.74
1.62-1.640.30672950.27647068X-RAY DIFFRACTION99.97
1.64-1.660.30222910.25086983X-RAY DIFFRACTION99.95
1.66-1.680.26792940.22697056X-RAY DIFFRACTION99.93
1.68-1.70.25662920.20217003X-RAY DIFFRACTION99.88
1.7-1.720.26022950.19717085X-RAY DIFFRACTION99.96
1.72-1.750.2242920.16586993X-RAY DIFFRACTION99.89
1.75-1.770.20662920.15317027X-RAY DIFFRACTION99.92
1.77-1.80.20822940.14767055X-RAY DIFFRACTION99.86
1.8-1.830.19372950.13967070X-RAY DIFFRACTION99.92
1.83-1.860.20332920.14836999X-RAY DIFFRACTION99.92
1.86-1.90.19672920.1597024X-RAY DIFFRACTION99.88
1.9-1.930.20222940.16127060X-RAY DIFFRACTION99.97
1.93-1.970.19572950.13697074X-RAY DIFFRACTION99.95
1.97-2.020.17772920.12247000X-RAY DIFFRACTION99.95
2.02-2.060.17782940.12087054X-RAY DIFFRACTION99.97
2.06-2.110.16412960.12287098X-RAY DIFFRACTION99.92
2.11-2.170.16522910.1196995X-RAY DIFFRACTION99.9
2.17-2.240.16142940.1187053X-RAY DIFFRACTION99.92
2.24-2.310.16562950.12217075X-RAY DIFFRACTION99.89
2.31-2.390.15662930.1197046X-RAY DIFFRACTION99.96
2.39-2.490.15262960.12267092X-RAY DIFFRACTION99.95
2.49-2.60.16892930.12777037X-RAY DIFFRACTION99.86
2.6-2.740.1762940.13757057X-RAY DIFFRACTION99.93
2.74-2.910.17222950.14287079X-RAY DIFFRACTION99.93
2.91-3.130.16522950.14697082X-RAY DIFFRACTION99.69
3.13-3.450.14422940.13847059X-RAY DIFFRACTION99.69
3.45-3.950.14172980.12597142X-RAY DIFFRACTION99.96
3.95-4.970.11172950.10077099X-RAY DIFFRACTION99.8
4.97-47.10.12923020.12587220X-RAY DIFFRACTION99.52

+
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