[English] 日本語
Yorodumi
- PDB-6tyr: Crystal structure of Laccase from Thermus thermophilus HB27 with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tyr
TitleCrystal structure of Laccase from Thermus thermophilus HB27 with a close conformation of its beta-hairpin
ComponentsLaccase
KeywordsOXIDOREDUCTASE / close loop / laccase / multicopper oxidase
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, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
CITRIC ACID / COPPER (II) ION / Laccase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.813 Å
AuthorsMiranda-Blancas, R. / Rudino-Pinera, E.
CitationJournal: J.Struct.Biol. / Year: 2021
Title: The beta-hairpin from the Thermus thermophilus HB27 laccase works as a pH-dependent switch to regulate laccase activity.
Authors: Miranda-Blancas, R. / Avelar, M. / Rodriguez-Arteaga, A. / Sinicropi, A. / Rudino-Pinera, E.
History
DepositionAug 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: 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: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4518
Polymers48,7911
Non-polymers6597
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein was loaded at superdex 75 column and eluted woth MES pH 5.5 20 mM and 50 mM NaCl
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.445, 85.386, 169.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-276-

ARG

-
Components

#1: Protein Laccase / multicopper oxidase


Mass: 48791.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria)
Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_C1370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72HW2, laccase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 277.15 K / Method: microbatch / pH: 5.5
Details: 20% PEG 4000, 20% 2-propanol, 100 mM sodium citrate pH 5.5
PH range: 5.5-5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 25, 2018 / Details: OSMIC VARIMAX CU-HF
RadiationMonochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→42.29 Å / Num. obs: 39303 / % possible obs: 96.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0307 / Rpim(I) all: 0.0307 / Rrim(I) all: 0.043 / Net I/σ(I): 25.62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.81-1.881.90.3472.934300.6820.3470.49185.4
1.88-1.951.90.2454.138130.820.2450.34695
1.95-2.041.90.1685.938450.8990.1680.23795.6
2.04-2.151.90.128.138620.9460.120.1796.5
2.15-2.281.90.0911.239430.9670.090.12796.9
2.28-2.461.90.06914.239410.9810.0690.09797.4
2.46-2.711.90.05418.839970.9870.0540.07798.7
2.71-3.120.0332.741010.9960.030.04399.8
3.1-3.9120.0255.841080.9980.020.02899.9
3.91-42.2920.01391.342630.9990.0130.01899.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACK7.0.076data scaling
PHASER7.0.076phasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XU9

2xu9


Resolution: 1.813→42.29 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.43
RfactorNum. reflection% reflection
Rfree0.2332 1908 4.86 %
Rwork0.1806 --
obs0.1831 39244 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.99 Å2 / Biso mean: 27.8254 Å2 / Biso min: 9.52 Å2
Refinement stepCycle: final / Resolution: 1.813→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 34 290 3763
Biso mean--41.24 36.28 -
Num. residues----439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8134-1.85870.3279950.2824223282
1.8587-1.9090.31191230.2656256394
1.909-1.96510.33871560.2358258595
1.9651-2.02860.28691370.2123263396
2.0286-2.10110.26351270.2136263096
2.1011-2.18520.24261540.2024263397
2.1852-2.28460.26351230.1976268297
2.2846-2.40510.24961250.1883268697
2.4051-2.55580.26041380.1921268398
2.5558-2.75310.23781360.1856276599
2.7531-3.030.21271420.1784272899
3.03-3.46830.22191540.16532787100
3.4683-4.3690.19711540.14522806100
4.369-42.290.20951440.1662923100

+
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