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- PDB-9j50: Crystal structure of the closed state of the omega transaminase T... -

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Basic information

Entry
Database: PDB / ID: 9j50
TitleCrystal structure of the closed state of the omega transaminase TA_5182 from Pseudomonas putida KT2440
ComponentsPolyamine:pyruvate transaminase
KeywordsTRANSFERASE / omega transaminase / aminotransferase / pseudomonas putida / thermal stability / 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
PHOSPHATE ION / Polyamine:pyruvate transaminase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDas, P. / Bhaumik, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural insights and rational design of Pseudomonas putida 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

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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)200,46012
Polymers199,7334
Non-polymers7278
Water77543
1
A: Polyamine:pyruvate transaminase
B: Polyamine:pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2466
Polymers99,8662
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-105 kcal/mol
Surface area29160 Å2
MethodPISA
2
C: Polyamine:pyruvate transaminase
D: Polyamine:pyruvate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2136
Polymers99,8662
Non-polymers3474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-98 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.570, 72.660, 106.910
Angle α, β, γ (deg.)95.67, 107.84, 109.19
Int Tables number1
Space group name H-MP1

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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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8.2 / Details: 1.4M Sodium Potassium Phosphate, pH 8.2

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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: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 44225 / % possible obs: 93.7 % / Redundancy: 1.99 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 5.8
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 8374 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.37 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.868 / SU B: 26.782 / SU ML: 0.48 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29741 2212 5 %RANDOM
Rwork0.24743 ---
obs0.24989 42013 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.465 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å25.42 Å2-0.34 Å2
2--1.77 Å23.16 Å2
3----4.2 Å2
Refinement stepCycle: 1 / Resolution: 2.8→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13913 0 39 45 13997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01214350
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613625
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.82319440
X-RAY DIFFRACTIONr_angle_other_deg0.4451.75631460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.92451807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.283584
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.097102427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0590.22085
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023186
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_it5.2557.5137199
X-RAY DIFFRACTIONr_mcbond_other5.2547.5137199
X-RAY DIFFRACTIONr_mcangle_it8.22613.5139000
X-RAY DIFFRACTIONr_mcangle_other8.22513.5139001
X-RAY DIFFRACTIONr_scbond_it4.4257.7727151
X-RAY DIFFRACTIONr_scbond_other4.4257.7727152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1914.22910435
X-RAY DIFFRACTIONr_long_range_B_refined12.88191.9260184
X-RAY DIFFRACTIONr_long_range_B_other12.8891.9260184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 164 -
Rwork0.407 3109 -
obs--94.73 %

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