[English] 日本語
Yorodumi
- PDB-6snl: (R)-selective amine transaminase from Exophiala sideris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6snl
Title(R)-selective amine transaminase from Exophiala sideris
Componentsamine transaminase
KeywordsTRANSFERASE / fold IV PLP-dependent enzyme / amine transaminase
Function / homologyAminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / catalytic activity / PYRIDOXAL-5'-PHOSPHATE / Uncharacterized protein
Function and homology information
Biological speciesExophiala sideris (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.129 Å
AuthorsTelzerow, A. / Hakansson, M. / Steiner, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
European Commission634200 Austria
CitationJournal: Chembiochem / Year: 2021
Title: Expanding the Toolbox of R-Selective Amine Transaminases by Identification and Characterization of New Members.
Authors: Telzerow, A. / Paris, J. / Hakansson, M. / Gonzalez-Sabin, J. / Rios-Lombardia, N. / Groger, H. / Moris, F. / Schurmann, M. / Schwab, H. / Steiner, K.
History
DepositionAug 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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: amine transaminase
B: amine transaminase
C: amine transaminase
D: amine transaminase
E: amine transaminase
F: amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,82417
Polymers231,8046
Non-polymers2,02011
Water19811
1
A: amine transaminase
D: amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8545
Polymers77,2682
Non-polymers5863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-27 kcal/mol
Surface area24910 Å2
MethodPISA
2
B: amine transaminase
hetero molecules

E: amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8545
Polymers77,2682
Non-polymers5863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z+1/21
Buried area5830 Å2
ΔGint-30 kcal/mol
Surface area24630 Å2
MethodPISA
3
C: amine transaminase
F: amine transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1167
Polymers77,2682
Non-polymers8485
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-52 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.113, 301.521, 140.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
amine transaminase


Mass: 38634.004 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exophiala sideris (fungus) / Gene: PV11_02554
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0D1XFW6

-
Non-polymers , 5 types, 22 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: NaCl, Bis-Tris, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.129→66.44 Å / Num. obs: 43551 / % possible obs: 99 % / Redundancy: 13.1 % / Biso Wilson estimate: 53.8 Å2 / CC1/2: 0.978 / Rpim(I) all: 0.1411 / Net I/σ(I): 5.22
Reflection shellResolution: 3.129→3.241 Å / Redundancy: 13 % / Mean I/σ(I) obs: 1.08 / Num. unique obs: 4277 / CC1/2: 0.621 / Rpim(I) all: 0.6867 / % possible all: 97.36

-
Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIX1.14-3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CE5
Resolution: 3.129→66.44 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2892 2067 4.78 %
Rwork0.2619 --
obs0.2631 43157 99.01 %
Displacement parametersBiso mean: 50.25 Å2
Refinement stepCycle: LAST / Resolution: 3.129→66.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14925 0 123 11 15059

+
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