[English] 日本語
Yorodumi
- PDB-9j4y: Crystal Structure of the L322F mutant of Omega Transaminase TA_27... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j4y
TitleCrystal Structure of the L322F mutant of Omega Transaminase TA_2799 from Pseudomonas putida KT2440
ComponentsAminotransferase, class III
KeywordsTRANSFERASE / Omega Transminase / aminotransferase / Pseudomonas / transaminase mutant / thermostability / PLP affinity
Function / homology
Function and homology information


gamma-aminobutyric acid metabolic process / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Aminotransferase, class III
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDas, P. / Bhaumik, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural insights and rational design of Pseudomonasputida KT2440 omega transaminases for enhanced biotransformation of (R)-PAC to (1R, 2S)-Norephedrine.
Authors: Das, P. / Noronha, S. / Bhaumik, P.
History
DepositionAug 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminotransferase, class III
B: Aminotransferase, class III
C: Aminotransferase, class III
D: Aminotransferase, class III
E: Aminotransferase, class III
F: Aminotransferase, class III
G: Aminotransferase, class III
H: Aminotransferase, class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)401,31934
Polymers399,1258
Non-polymers2,19426
Water5,368298
1
A: Aminotransferase, class III
B: Aminotransferase, class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,48611
Polymers99,7812
Non-polymers7059
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12610 Å2
ΔGint-99 kcal/mol
Surface area28490 Å2
MethodPISA
2
C: Aminotransferase, class III
D: Aminotransferase, class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,49810
Polymers99,7812
Non-polymers7178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-119 kcal/mol
Surface area28570 Å2
MethodPISA
3
E: Aminotransferase, class III
F: Aminotransferase, class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0986
Polymers99,7812
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-108 kcal/mol
Surface area28690 Å2
MethodPISA
4
G: Aminotransferase, class III
H: Aminotransferase, class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2387
Polymers99,7812
Non-polymers4565
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-113 kcal/mol
Surface area28710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.160, 121.440, 147.410
Angle α, β, γ (deg.)90.00, 111.88, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Aminotransferase, class III


Mass: 49890.633 Da / Num. of mol.: 8 / Mutation: L322F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: PP_2799 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88J50

-
Non-polymers , 5 types, 324 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Lithium sulphate, 0.1M bis-Tris pH 5.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9789 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 133254 / % possible obs: 98.8 % / Redundancy: 3.89 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.71
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 1.18 / Num. unique obs: 14679

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 12.1 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 0.731 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23279 6663 5 %RANDOM
Rwork0.19428 ---
obs0.19621 126588 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.907 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-1.03 Å2
2--1.58 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.5→39.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27900 0 129 298 28327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01228754
X-RAY DIFFRACTIONr_bond_other_d0.0010.01627096
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.79239156
X-RAY DIFFRACTIONr_angle_other_deg0.4471.73362090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64653643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.7345188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.887104361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.24395
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0234458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026814
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9063.89114554
X-RAY DIFFRACTIONr_mcbond_other4.9063.89114554
X-RAY DIFFRACTIONr_mcangle_it7.0036.98218182
X-RAY DIFFRACTIONr_mcangle_other7.0036.98218183
X-RAY DIFFRACTIONr_scbond_it5.4224.24914200
X-RAY DIFFRACTIONr_scbond_other5.4224.24914201
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7527.64220968
X-RAY DIFFRACTIONr_long_range_B_refined9.46437.7931792
X-RAY DIFFRACTIONr_long_range_B_other9.46537.831777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 486 -
Rwork0.327 9242 -
obs--98.63 %

+
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