[English] 日本語
Yorodumi
- PDB-4j6t: Crystal Structure of Tyrosinase from Bacillus megaterium F197A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j6t
TitleCrystal Structure of Tyrosinase from Bacillus megaterium F197A mutant
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / type 3 copper proteins
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / : / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Tyrosinase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.43 Å
AuthorsKanteev, M. / Goldfeder, M. / Adir, N. / Fishman, A.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2013
Title: The mechanism of copper uptake by tyrosinase from Bacillus megaterium.
Authors: Kanteev, M. / Goldfeder, M. / Chojnacki, M. / Adir, N. / Fishman, A.
#1: Journal: J.Mol.Biol. / Year: 2011
Title: First structures of an active bacterial tyrosinase reveal copper plasticity.
Authors: Sendovski, M. / Kanteev, M. / Ben-Yosef, V.S. / Adir, N. / Fishman, A.
History
DepositionFeb 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6116
Polymers70,3572
Non-polymers2544
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.010, 78.810, 84.340
Angle α, β, γ (deg.)90.000, 106.620, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Tyrosinase


Mass: 35178.379 Da / Num. of mol.: 2 / Mutation: F197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2ZB02, tyrosinase
#2: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.49 Å3/Da / Density % sol: 50.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, pH 6.5, 18% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.43→80.817 Å / Num. all: 26006 / Num. obs: 26006 / % possible obs: 99.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 7.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.43-2.562.90.1693.81081237320.16998.1
2.56-2.723.30.1553.91176235970.155100
2.72-2.93.20.1374.41103834110.137100
2.9-3.143.20.1274.51012031200.127100
3.14-3.443.20.1095.4938729150.10999.9
3.44-3.843.10.1313.4823126140.13199.9
3.84-4.443.10.0876.5728523130.08799.6
4.44-5.433.10.0837608919650.08399.5
5.43-7.682.80.0757.4429915260.07599.3
7.68-27.4813.30.0757.426468130.07594.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.75 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.48 Å
Translation2.5 Å27.48 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NM8

3nm8


Resolution: 2.43→27.481 Å / Occupancy max: 1 / Occupancy min: 0.6 / FOM work R set: 0.8312 / SU ML: 0.37 / σ(F): 1.36 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2375 1318 5.08 %
Rwork0.1961 --
obs0.1983 25932 99.14 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.462 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 107.64 Å2 / Biso mean: 33.0452 Å2 / Biso min: 12.33 Å2
Baniso -1Baniso -2Baniso -3
1-4.1595 Å20 Å2-1.1544 Å2
2--1.005 Å20 Å2
3----5.1644 Å2
Refinement stepCycle: LAST / Resolution: 2.43→27.481 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4688 0 4 207 4899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164860
X-RAY DIFFRACTIONf_angle_d1.1866625
X-RAY DIFFRACTIONf_chiral_restr0.081661
X-RAY DIFFRACTIONf_plane_restr0.006878
X-RAY DIFFRACTIONf_dihedral_angle_d16.2891775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.43-2.52740.3311330.25162676280997
2.5274-2.64230.33871440.239827252869100
2.6423-2.78150.29471540.225127312885100
2.7815-2.95560.26481420.216127462888100
2.9556-3.18340.26061320.213127432875100
3.1834-3.50320.25551600.217727262886100
3.5032-4.00880.24481530.20832745289899
4.0088-5.04560.16421510.14962764291599
5.0456-27.48270.19841490.15912758290798
Refinement TLS params.Method: refined / Origin x: 12.9484 Å / Origin y: -12.83 Å / Origin z: 24.9767 Å
111213212223313233
T0.0981 Å2-0.0145 Å20.0227 Å2-0.1149 Å2-0.0034 Å2--0.1389 Å2
L0.2451 °2-0.0654 °20.2281 °2-0.4105 °20.0766 °2--1.1161 °2
S0.007 Å °-0.0334 Å °0.0382 Å °0.0138 Å °0.0123 Å °0.0218 Å °0.0318 Å °0.081 Å °-0.0112 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 521
2X-RAY DIFFRACTION1allB4 - 486

+
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