[English] 日本語
Yorodumi
- PDB-8xiy: Crystal structure of an omega-transaminase mutant I77L/Q97E/H210N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xiy
TitleCrystal structure of an omega-transaminase mutant I77L/Q97E/H210N/N245D from Aspergillus terreus in complex with PLP
ComponentsD-aminoacid aminotransferase-like PLP-dependent enzyme
KeywordsTRANSFERASE / omega-transaminase / furfuramine / TRANSLOCASE
Function / homology
Function and homology information


carboxylic acid biosynthetic process / amino acid biosynthetic process / catalytic activity / metal ion binding
Similarity search - Function
: / Branched-chain-amino-acid aminotransferase-like, N-terminal / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / D-aminoacid aminotransferase-like PLP-dependent enzyme
Similarity search - Component
Biological speciesAspergillus terreus NIH2624 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLu, Z.Y. / Hu, D. / Xu, D.Z. / He, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21978072 China
CitationJournal: To Be Published
Title: Efficient bioamination with an omega-transaminase mutant from Aspergillus terreus
Authors: He, Y.C.
History
DepositionDec 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: D-aminoacid aminotransferase-like PLP-dependent enzyme
B: D-aminoacid aminotransferase-like PLP-dependent enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2504
Polymers74,7552
Non-polymers4942
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.420, 135.790, 116.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

21B-741-

HOH

-
Components

#1: Protein D-aminoacid aminotransferase-like PLP-dependent enzyme


Mass: 37377.656 Da / Num. of mol.: 2 / Mutation: I77L,Q97E,H210N,N245D
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL-5-PHOSPHATE (three-letter code PLP / Source: (gene. exp.) Aspergillus terreus NIH2624 (mold) / Gene: ATEG_10023 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0C8G1
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM citrate buffer (pH 7.5) 200 mM ammonium acetate 4% (w/v) PEG-MME 8000 1 mM pyridoxal phosphate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.09→41.881 Å / Num. obs: 49080 / % possible obs: 97.5 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.034 / Rrim(I) all: 0.114 / Net I/σ(I): 16.4
Reflection shellResolution: 2.09→9.35 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.875 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3025 / Rpim(I) all: 0.441 / Rrim(I) all: 0.987 / % possible all: 82.9

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
AMPLEphasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→41.881 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2416 4.93 %
Rwork0.1711 --
obs0.1733 49044 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→41.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 32 497 5515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085132
X-RAY DIFFRACTIONf_angle_d0.8186980
X-RAY DIFFRACTIONf_dihedral_angle_d12.193038
X-RAY DIFFRACTIONf_chiral_restr0.056774
X-RAY DIFFRACTIONf_plane_restr0.006902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.13270.30321170.26952263X-RAY DIFFRACTION81
2.1327-2.17910.30141230.24882415X-RAY DIFFRACTION87
2.1791-2.22970.2891430.22882561X-RAY DIFFRACTION92
2.2297-2.28550.24161280.21622667X-RAY DIFFRACTION96
2.2855-2.34730.27251450.19552799X-RAY DIFFRACTION99
2.3473-2.41630.24921670.1892741X-RAY DIFFRACTION100
2.4163-2.49430.25321310.18552804X-RAY DIFFRACTION100
2.4943-2.58350.21751530.17822790X-RAY DIFFRACTION100
2.5835-2.68690.26261610.17552810X-RAY DIFFRACTION100
2.6869-2.80920.23991310.17812808X-RAY DIFFRACTION100
2.8092-2.95720.22351290.18152833X-RAY DIFFRACTION100
2.9572-3.14240.19451460.16462806X-RAY DIFFRACTION100
3.1424-3.3850.22141200.15872851X-RAY DIFFRACTION100
3.385-3.72540.19681510.14962827X-RAY DIFFRACTION100
3.7254-4.2640.1821550.13752837X-RAY DIFFRACTION100
4.264-5.37050.17291620.1432850X-RAY DIFFRACTION99
5.3705-41.880.2121540.18612966X-RAY DIFFRACTION100

+
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