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- PDB-9j2k: Crystal structure of Omega Transaminase TA_2799 from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 9j2k
TitleCrystal structure of Omega Transaminase TA_2799 from Pseudomonas putida KT2440
ComponentsAminotransferase, class III
KeywordsTRANSFERASE / omega transaminase / aminotransferase / pseudomonas / PLP / thermal stability / fold type I
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 / MOLECULAR REPLACEMENT / Resolution: 1.76 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 7, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase, class III
B: Aminotransferase, class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,58118
Polymers100,1692
Non-polymers1,41116
Water17,132951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14380 Å2
ΔGint-62 kcal/mol
Surface area28740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.000, 92.790, 136.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminotransferase, class III / Omega Transaminase


Mass: 50084.734 Da / Num. of mol.: 2
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, EC: 2.6.1.96
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 951 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, 2% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→44.31 Å / Num. obs: 94029 / % possible obs: 99.2 % / Redundancy: 6.31 % / CC1/2: 0.99 / Net I/σ(I): 18.46
Reflection shellResolution: 1.76→1.81 Å / Num. unique obs: 6834 / CC1/2: 0.96 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→44.31 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 4700 5 %RANDOM
Rwork0.1454 ---
obs0.1468 94014 99.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6989 0 122 951 8062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067436
X-RAY DIFFRACTIONf_angle_d0.87210138
X-RAY DIFFRACTIONf_dihedral_angle_d14.9052705
X-RAY DIFFRACTIONf_chiral_restr0.0551130
X-RAY DIFFRACTIONf_plane_restr0.0071326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.780.26411540.20042921X-RAY DIFFRACTION97
1.78-1.80.22961530.19062904X-RAY DIFFRACTION99
1.8-1.820.21191550.17422956X-RAY DIFFRACTION99
1.82-1.850.18971550.172938X-RAY DIFFRACTION99
1.85-1.870.21941560.15542960X-RAY DIFFRACTION99
1.87-1.90.18871550.15232954X-RAY DIFFRACTION99
1.9-1.920.18371560.14942963X-RAY DIFFRACTION99
1.92-1.950.19331530.14312910X-RAY DIFFRACTION99
1.95-1.980.17791550.14352939X-RAY DIFFRACTION99
1.98-2.010.19641560.152970X-RAY DIFFRACTION99
2.01-2.050.19091560.15022947X-RAY DIFFRACTION99
2.05-2.090.18491560.14842973X-RAY DIFFRACTION99
2.09-2.130.17781550.14752948X-RAY DIFFRACTION99
2.13-2.170.19281540.14652931X-RAY DIFFRACTION99
2.17-2.220.16531570.14542968X-RAY DIFFRACTION99
2.22-2.270.1661570.14572992X-RAY DIFFRACTION99
2.27-2.330.17841560.14642963X-RAY DIFFRACTION99
2.33-2.390.17721560.13982963X-RAY DIFFRACTION99
2.39-2.460.18491550.14772952X-RAY DIFFRACTION99
2.46-2.540.16781570.14282973X-RAY DIFFRACTION99
2.54-2.630.17971570.14832992X-RAY DIFFRACTION99
2.63-2.730.19341570.14372977X-RAY DIFFRACTION99
2.73-2.860.17721570.14072981X-RAY DIFFRACTION99
2.86-3.010.18081580.15072995X-RAY DIFFRACTION99
3.01-3.20.1481570.1423000X-RAY DIFFRACTION99
3.2-3.440.17171580.13773001X-RAY DIFFRACTION99
3.44-3.790.14871580.13413014X-RAY DIFFRACTION99
3.79-4.340.14621600.12323033X-RAY DIFFRACTION99
4.34-5.460.14461620.13123082X-RAY DIFFRACTION99
5.47-44.310.18891690.16293214X-RAY DIFFRACTION99

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