[English] 日本語
Yorodumi
- PDB-8gyi: Crystal structure of Fic25 (holo form) from Streptomyces ficellus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gyi
TitleCrystal structure of Fic25 (holo form) from Streptomyces ficellus
ComponentsDegT/DnrJ/EryC1/StrS family aminotransferase
KeywordsBIOSYNTHETIC PROTEIN / Sugar aminotransferase / Biosynthetic enzyme / DADH
Function / homology
Function and homology information


polysaccharide biosynthetic process / transaminase activity / antibiotic biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
IMIDAZOLE / PYRIDOXAL-5'-PHOSPHATE / DegT/DnrJ/EryC1/StrS family aminotransferase
Similarity search - Component
Biological speciesStreptomyces ficellus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKurosawa, S. / Yoshida, A. / Tomita, T. / Nishiyama, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24228001 Japan
Japan Society for the Promotion of Science (JSPS)17H06168 Japan
Japan Society for the Promotion of Science (JSPS)22H00355 Japan
Japan Science and TechnologyJPMJSP2108 Japan
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Mechanisms of Sugar Aminotransferase-like Enzymes to Synthesize Stereoisomers of Non-proteinogenic Amino Acids in Natural Product Biosynthesis.
Authors: Kurosawa, S. / Okamura, H. / Yoshida, A. / Tomita, T. / Sone, Y. / Hasebe, F. / Shinada, T. / Takikawa, H. / Kosono, S. / Nishiyama, M.
History
DepositionSep 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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: DegT/DnrJ/EryC1/StrS family aminotransferase
B: DegT/DnrJ/EryC1/StrS family aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,75510
Polymers93,8242
Non-polymers9328
Water13,601755
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6860 Å2
ΔGint-26 kcal/mol
Surface area29840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.628, 201.628, 57.009
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein DegT/DnrJ/EryC1/StrS family aminotransferase / Glutamine--scyllo-inositol transaminase / Fic25


Mass: 46911.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ficellus (bacteria) / Gene: EIZ62_06105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W5T2G9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 755 / 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: 3.57 Å3/Da / Density % sol: 65.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.0 M Sodium citrate, 0.1 M Imidazole, pH 8.0

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→48.48 Å / Num. obs: 99447 / % possible obs: 99.5 % / Redundancy: 10.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.3
Reflection shellResolution: 1.93→1.96 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4853 / CC1/2: 0.817

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GYH

8gyh


Resolution: 1.93→48.48 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.735 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1878 4946 5 %RANDOM
Rwork0.1666 ---
obs0.1677 94493 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.96 Å2 / Biso mean: 24.539 Å2 / Biso min: 12.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.35 Å20 Å2
2--0.71 Å2-0 Å2
3----2.3 Å2
Refinement stepCycle: final / Resolution: 1.93→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6299 0 61 755 7115
Biso mean--32.69 33.76 -
Num. residues----839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0136616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176145
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.6429025
X-RAY DIFFRACTIONr_angle_other_deg1.1651.57214138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0265858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.07420.028363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20915960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7251569
X-RAY DIFFRACTIONr_chiral_restr0.0490.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021514
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 378 -
Rwork0.246 6873 -
all-7251 -
obs--98.45 %

+
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