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- PDB-9j4z: Crystal structure of the open state of omega transaminase TA_5182... -

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Basic information

Entry
Database: PDB / ID: 9j4z
TitleCrystal structure of the open state of omega transaminase TA_5182 from Pseudomonas putida KT2440
ComponentsPolyamine:pyruvate transaminase
KeywordsTRANSFERASE / omega transaminase / aminotransferase / thermal stability / pseudomonas putida / cofactor 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
Polyamine:pyruvate transaminase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyamine:pyruvate transaminase
B: Polyamine:pyruvate transaminase
C: Polyamine:pyruvate transaminase
D: Polyamine:pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,98217
Polymers199,7334
Non-polymers1,24913
Water00
1
A: Polyamine:pyruvate transaminase
B: Polyamine:pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,73111
Polymers99,8662
Non-polymers8659
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-161 kcal/mol
Surface area30230 Å2
MethodPISA
2
C: Polyamine:pyruvate transaminase
D: Polyamine:pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2516
Polymers99,8662
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-83 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.030, 151.340, 156.650
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
Polyamine:pyruvate transaminase


Mass: 49933.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: spuC-II, PP_5182 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q88CJ8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN
Has protein modificationN

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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: 2.82 Å3/Da / Density % sol: 61.75 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis-Tris pH 5.5, 2M ammonium sulphate

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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: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 31744 / % possible obs: 99.9 % / Redundancy: 7.35 % / CC1/2: 0.986 / Net I/σ(I): 6.16
Reflection shellResolution: 3.4→3.5 Å / Num. unique obs: 2594 / CC1/2: 0.566 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.02 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.879 / SU B: 30.962 / SU ML: 0.463 / Cross valid method: THROUGHOUT / ESU R Free: 0.572 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25801 1588 5 %RANDOM
Rwork0.20569 ---
obs0.20825 30155 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.102 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å2-0 Å2
2---3.1 Å20 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 3.4→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12318 0 65 0 12383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01212657
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612109
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.82217141
X-RAY DIFFRACTIONr_angle_other_deg0.4451.75627919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36251577
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.486579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.592102138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0570.21873
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022797
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_it8.569.1036332
X-RAY DIFFRACTIONr_mcbond_other8.569.1036332
X-RAY DIFFRACTIONr_mcangle_it13.55616.3497901
X-RAY DIFFRACTIONr_mcangle_other13.55516.357902
X-RAY DIFFRACTIONr_scbond_it7.8699.5566325
X-RAY DIFFRACTIONr_scbond_other7.8019.5176274
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.84517.3719163
X-RAY DIFFRACTIONr_long_range_B_refined18.23884.3314223
X-RAY DIFFRACTIONr_long_range_B_other18.23884.3314223
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 114 -
Rwork0.308 2160 -
obs--99.96 %

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