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- PDB-9j4y: Crystal Structure of the L322F mutant of Omega Transaminase TA_27... -

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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 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

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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

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Components

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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

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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

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Details

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: 2.48 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

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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

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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 %

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