[English] 日本語
Yorodumi
- PDB-9ivh: Structure of TF9 mutant of aminotransferase from Mycolicibacteriu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ivh
TitleStructure of TF9 mutant of aminotransferase from Mycolicibacterium neoaurum in complex with LLP and G4O
ComponentsBranched-chain amino acid transferase
KeywordsTRANSFERASE / complex
Function / homology
Function and homology information


carboxylic acid biosynthetic process / transferase activity
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
propan-2-amine / Branched-chain amino acid transferase
Similarity search - Component
Biological speciesMycolicibacterium neoaurum VKM Ac-1815D (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsWei, H. / Cong, L. / You, S. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structure of TF9 mutant of aminotransferase from Mycolicibacterium neoaurum in complex with LLP and G4O
Authors: Wei, H. / Cong, L. / You, S. / Liu, W.
History
DepositionJul 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Branched-chain amino acid transferase
B: Branched-chain amino acid transferase
C: Branched-chain amino acid transferase
D: Branched-chain amino acid transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,7968
Polymers142,5594
Non-polymers2364
Water17,439968
1
A: Branched-chain amino acid transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6992
Polymers35,6401
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Branched-chain amino acid transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6992
Polymers35,6401
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Branched-chain amino acid transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6992
Polymers35,6401
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Branched-chain amino acid transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6992
Polymers35,6401
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Branched-chain amino acid transferase
C: Branched-chain amino acid transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3984
Polymers71,2802
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-22 kcal/mol
Surface area23560 Å2
MethodPISA
6
B: Branched-chain amino acid transferase
D: Branched-chain amino acid transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3984
Polymers71,2802
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-23 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.615, 78.586, 91.541
Angle α, β, γ (deg.)96.96, 108.42, 113.07
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Branched-chain amino acid transferase


Mass: 35639.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium neoaurum VKM Ac-1815D (bacteria)
Gene: D174_04695
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: V5X927
#2: Chemical
ChemComp-G4O / propan-2-amine


Mass: 59.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H9N / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 968 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Cacodylate pH 6.5,0.2 M MgCl2,10 %PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9787 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.02→42.55 Å / Num. obs: 94474 / % possible obs: 92.25 % / Redundancy: 2.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.097 / Net I/σ(I): 2.2
Reflection shellResolution: 2.02→2.13 Å / Rmerge(I) obs: 0.507 / Num. unique obs: 14021 / CC1/2: 0.825 / Rpim(I) all: 0.348

-
Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→42.55 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.8 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 4700 4.98 %
Rwork0.2001 --
obs0.2021 94442 92.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9666 0 16 968 10650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.235
X-RAY DIFFRACTIONf_dihedral_angle_d7.9951385
X-RAY DIFFRACTIONf_chiral_restr0.091488
X-RAY DIFFRACTIONf_plane_restr0.0191765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.090.32754820.27449093X-RAY DIFFRACTION94
2.09-2.170.32034720.26159074X-RAY DIFFRACTION93
2.17-2.270.31034590.25839060X-RAY DIFFRACTION94
2.27-2.390.29064780.24389106X-RAY DIFFRACTION93
2.39-2.540.30654820.24238991X-RAY DIFFRACTION92
2.54-2.740.28474670.23188949X-RAY DIFFRACTION92
2.74-3.010.24934720.21049065X-RAY DIFFRACTION93
3.01-3.450.22854660.18848849X-RAY DIFFRACTION91
3.45-4.340.18494530.16248811X-RAY DIFFRACTION90
4.34-42.550.1974690.16188744X-RAY DIFFRACTION90

+
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