[English] 日本語
Yorodumi
- PDB-7dbe: Structure of a novel transaminase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dbe
TitleStructure of a novel transaminase
Componentsbranched-chain amino acid aminotransferase
KeywordsTRANSFERASE / transaminase
Function / homologyPYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesRhodobacter sp. 140A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, F.L. / Yu, H.M.
CitationJournal: Adv.Synth.Catal. / Year: 2021
Title: Biochemical and Structural Characterization of an (R)-Selective Transaminase in the Asymmetric Synthesis of Chiral Hydroxy Amines.
Authors: Li, F.L. / Liang, Y.X. / Wei, Y.W. / Zheng, Y.K. / Yu, H.M.
History
DepositionOct 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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: branched-chain amino acid aminotransferase
B: branched-chain amino acid aminotransferase
C: branched-chain amino acid aminotransferase
D: branched-chain amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,97612
Polymers150,7404
Non-polymers1,2378
Water28,4101577
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.267, 141.074, 90.755
Angle α, β, γ (deg.)90.000, 100.111, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein
branched-chain amino acid aminotransferase


Mass: 37684.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sp. 140A (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1577 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsSequence has been deposited to Genbank with accession ID RBP85366. N-terminal residues MHHHHHH are ...Sequence has been deposited to Genbank with accession ID RBP85366. N-terminal residues MHHHHHH are from expression tag.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2% v/v Tacsimate pH 7.0, 5% v/v 2-Propanol, 0.1M Imidazole pH 7.0, 8% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 120439 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.61 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.053 / Rrim(I) all: 0.142 / Rsym value: 0.131 / Net I/σ(I): 18.7
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6029 / CC1/2: 0.565 / Rpim(I) all: 0.267 / Rrim(I) all: 0.721 / Rsym value: 0.665

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WWH

3wwh


Resolution: 1.9→46.85 Å / SU ML: 0.1861 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9076 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2013 6236 5.19 %
Rwork0.1601 113992 -
obs0.1622 120228 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10184 0 76 1577 11837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006610497
X-RAY DIFFRACTIONf_angle_d0.793614276
X-RAY DIFFRACTIONf_chiral_restr0.05741570
X-RAY DIFFRACTIONf_plane_restr0.00581856
X-RAY DIFFRACTIONf_dihedral_angle_d14.6396164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.27512110.23353694X-RAY DIFFRACTION98.21
1.92-1.940.24831950.21453881X-RAY DIFFRACTION99.95
1.94-1.970.21332220.18943742X-RAY DIFFRACTION99.67
1.97-1.990.23542130.18493787X-RAY DIFFRACTION99.75
1.99-2.020.22182160.18363855X-RAY DIFFRACTION99.75
2.02-2.050.24061960.18143771X-RAY DIFFRACTION99.42
2.05-2.080.27452180.2013795X-RAY DIFFRACTION99.65
2.08-2.110.22131910.17273806X-RAY DIFFRACTION99.97
2.11-2.140.23731950.16753883X-RAY DIFFRACTION99.93
2.14-2.180.22062100.16773752X-RAY DIFFRACTION99.7
2.18-2.210.222100.16663831X-RAY DIFFRACTION99.75
2.21-2.250.23092240.17233757X-RAY DIFFRACTION99.67
2.25-2.30.2091920.16713867X-RAY DIFFRACTION99.68
2.3-2.340.21192090.1613772X-RAY DIFFRACTION99.65
2.34-2.390.21342260.16353811X-RAY DIFFRACTION99.46
2.39-2.450.22912040.16883767X-RAY DIFFRACTION99.45
2.45-2.510.23092030.17183812X-RAY DIFFRACTION98.79
2.51-2.580.22782140.1643807X-RAY DIFFRACTION99.98
2.58-2.650.20362000.15893797X-RAY DIFFRACTION99.83
2.65-2.740.19952170.15833797X-RAY DIFFRACTION99.78
2.74-2.840.20652280.16143816X-RAY DIFFRACTION99.51
2.84-2.950.19222300.15563771X-RAY DIFFRACTION99.53
2.95-3.090.20421870.16143811X-RAY DIFFRACTION99.38
3.09-3.250.1951970.15533777X-RAY DIFFRACTION98.29
3.25-3.450.21242040.15523818X-RAY DIFFRACTION99.7
3.45-3.720.18312050.14543836X-RAY DIFFRACTION99.73
3.72-4.090.1782040.13663832X-RAY DIFFRACTION99.68
4.09-4.680.14672040.12713770X-RAY DIFFRACTION98.29
4.68-5.90.17461980.15093819X-RAY DIFFRACTION98.7
5.9-46.850.18712130.17473758X-RAY DIFFRACTION96.41

+
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