[English] 日本語
Yorodumi
- PDB-5k5k: Crystal structure of laccasse from Thermus thermophilus HB27 (asc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k5k
TitleCrystal structure of laccasse from Thermus thermophilus HB27 (ascorbic acid 10 min)
ComponentsLaccase
KeywordsOXIDOREDUCTASE / multicopper oxidases
Function / homology
Function and homology information


hydroquinone:oxygen oxidoreductase activity / laccase / outer membrane-bounded periplasmic space / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Laccase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsDiaz-Vilchis, A. / Ruiz-Arellano, R.R. / Rosas-Benitez, E. / Rudino-Pinera, E.
Funding support Mexico, 1items
OrganizationGrant numberCountry
UNAMDGAPA IN 209114-3 Mexico
CitationJournal: To be Published
Title: Preserving metallic sites affected by radiation damage: the CuT2 case in Thermus thermophilus multicopper oxidase
Authors: Diaz-Vilchis, A. / Ruiz-Arellano, R.R. / Rosas-Benitez, E. / Stojanoff, V. / Rudino-Pinera, E.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,40016
Polymers48,7911
Non-polymers1,60915
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-104 kcal/mol
Surface area17520 Å2
Unit cell
Length a, b, c (Å)93.440, 109.860, 96.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Laccase


Mass: 48791.457 Da / Num. of mol.: 1 / Fragment: UNP residues 24-462
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 (E. coli) / References: UniProt: Q72HW2, laccase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M HEPES, pH 7.5, 70% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 3, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.796→19.632 Å / Num. obs: 42011 / % possible obs: 91.2 % / Observed criterion σ(I): 3.66 / Redundancy: 2.45 % / Biso Wilson estimate: 13.63 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.83
Reflection shellResolution: 1.796→1.9 Å / Redundancy: 2.39 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.02 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2XU9

2xu9


Resolution: 1.796→19.632 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.58 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2159 2153 5.12 %
Rwork0.1752 39858 -
obs0.1773 42011 90.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.87 Å2 / Biso mean: 20.1967 Å2 / Biso min: 2.91 Å2
Refinement stepCycle: final / Resolution: 1.796→19.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3439 0 99 332 3870
Biso mean--56.13 31.79 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064298
X-RAY DIFFRACTIONf_angle_d0.9375952
X-RAY DIFFRACTIONf_chiral_restr0.053651
X-RAY DIFFRACTIONf_plane_restr0.006798
X-RAY DIFFRACTIONf_dihedral_angle_d24.831687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7955-1.83730.33971180.28192463258184
1.8373-1.88320.34561550.27462722287794
1.8832-1.93410.29531410.26412705284694
1.9341-1.99090.2841460.23572723286994
1.9909-2.05510.28161480.21942710285893
2.0551-2.12850.26411380.20342710284892
2.1285-2.21360.21851360.18612698283493
2.2136-2.31420.22611480.17942673282192
2.3142-2.4360.21161700.17352660283092
2.436-2.58830.22511520.17392685283792
2.5883-2.78760.23221390.16492668280791
2.7876-3.06720.20391460.1542648279490
3.0672-3.50890.18161290.1422653278290
3.5089-4.41250.14791430.12292612275587
4.4125-19.63340.16311440.1452528267282

+
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