[English] 日本語
Yorodumi
- PDB-6rh9: Crystal Structure of Two-Domain Laccase mutant I170F from Strepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rh9
TitleCrystal Structure of Two-Domain Laccase mutant I170F 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 / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / OXYGEN MOLECULE / Two-domain laccase
Similarity search - Component
Biological speciesStreptomyces griseoflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Kolyadenko, I.A.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-04-00270a Russian Federation
RAS program "Molecular and Cell Biology and Postgenomic Technologies"
CitationJournal: Int J Mol Sci / Year: 2019
Title: Investigations of Accessibility of T2/T3 Copper Center of Two-Domain Laccase fromStreptomyces griseoflavusAc-993.
Authors: Gabdulkhakov, A. / Kolyadenko, I. / Kostareva, O. / Mikhaylina, A. / Oliveira, P. / Tamagnini, P. / Lisov, A. / Tishchenko, S.
History
DepositionApr 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
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
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,54170
Polymers417,83612
Non-polymers3,70558
Water8,485471
1
A: Two-domain laccase
B: Two-domain laccase
C: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,28416
Polymers104,4593
Non-polymers82513
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-141 kcal/mol
Surface area27760 Å2
MethodPISA
2
D: Two-domain laccase
E: Two-domain laccase
F: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,38017
Polymers104,4593
Non-polymers92114
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-159 kcal/mol
Surface area27220 Å2
MethodPISA
3
G: Two-domain laccase
H: Two-domain laccase
I: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,47019
Polymers104,4593
Non-polymers1,01116
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-137 kcal/mol
Surface area27150 Å2
MethodPISA
4
J: Two-domain laccase
K: Two-domain laccase
L: Two-domain laccase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,40818
Polymers104,4593
Non-polymers94915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12050 Å2
ΔGint-143 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.250, 94.770, 116.180
Angle α, β, γ (deg.)90.13, 89.95, 92.56
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Two-domain laccase


Mass: 34819.668 Da / Num. of mol.: 12 / Mutation: I170F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces griseoflavus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4FJ81, laccase

-
Non-polymers , 6 types, 529 molecules

#2: Chemical...
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% Smear medium PEG, 0.1 M Bicine, 0.1 M NaCl, 0.05M H3BO3-NaOH

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 256815 / % possible obs: 91.4 % / Redundancy: 2.08 % / Rrim(I) all: 0.109 / Net I/σ(I): 10.9
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 12984

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O4Q

5o4q


Resolution: 1.85→47.337 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 28.66
RfactorNum. reflection% reflection
Rfree0.237 12840 5 %
Rwork0.1785 --
obs0.1814 256747 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→47.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25540 0 89 471 26100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826438
X-RAY DIFFRACTIONf_angle_d0.87435905
X-RAY DIFFRACTIONf_dihedral_angle_d20.5749391
X-RAY DIFFRACTIONf_chiral_restr0.0533651
X-RAY DIFFRACTIONf_plane_restr0.0054805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8710.39292770.35785256X-RAY DIFFRACTION59
1.871-1.8930.36582990.33775699X-RAY DIFFRACTION64
1.893-1.91610.39333250.32856170X-RAY DIFFRACTION70
1.9161-1.94030.38233810.31897234X-RAY DIFFRACTION81
1.9403-1.96590.35664390.30238341X-RAY DIFFRACTION93
1.9659-1.99280.36624430.28248404X-RAY DIFFRACTION95
1.9928-2.02130.33044490.27698544X-RAY DIFFRACTION95
2.0213-2.05140.34974460.26518453X-RAY DIFFRACTION95
2.0514-2.08350.31794450.25218462X-RAY DIFFRACTION95
2.0835-2.11770.30494470.25058487X-RAY DIFFRACTION96
2.1177-2.15420.31124450.24098455X-RAY DIFFRACTION95
2.1542-2.19330.29954460.2388478X-RAY DIFFRACTION95
2.1933-2.23550.32484440.248423X-RAY DIFFRACTION95
2.2355-2.28120.31714460.23248506X-RAY DIFFRACTION95
2.2812-2.33080.28934520.22798569X-RAY DIFFRACTION96
2.3308-2.3850.29714470.20238493X-RAY DIFFRACTION96
2.385-2.44460.26934500.20438551X-RAY DIFFRACTION96
2.4446-2.51070.28464470.20828495X-RAY DIFFRACTION96
2.5107-2.58460.30464510.20888568X-RAY DIFFRACTION95
2.5846-2.6680.29284420.20558388X-RAY DIFFRACTION94
2.668-2.76330.28034370.19658300X-RAY DIFFRACTION93
2.7633-2.8740.26154440.18918435X-RAY DIFFRACTION95
2.874-3.00470.25554400.17038366X-RAY DIFFRACTION95
3.0047-3.16310.24174460.15128463X-RAY DIFFRACTION95
3.1631-3.36130.21174450.15268462X-RAY DIFFRACTION95
3.3613-3.62070.19934380.13988315X-RAY DIFFRACTION94
3.6207-3.98490.18294450.12978450X-RAY DIFFRACTION95
3.9849-4.56110.14884390.11518359X-RAY DIFFRACTION94
4.5611-5.74490.14914340.12438241X-RAY DIFFRACTION93
5.7449-47.3530.18744510.17248540X-RAY DIFFRACTION96

+
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