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- PDB-9wf1: PLP and 1-Boc-2-methyl-piperidin-5-one complex structure of an (R... -

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Basic information

Entry
Database: PDB / ID: 9wf1
TitlePLP and 1-Boc-2-methyl-piperidin-5-one complex structure of an (R)-selective omega-transaminase from Ancylobacter lacus
ComponentsOmega-Transaminase
KeywordsTRANSFERASE / (R)-selective omega-transaminase / Complex with PLP and 1-Boc-2-methyl-piperidin-5-one
Function / homology:
Function and homology information
Biological speciesAncylobacter lacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsLin, S. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2026
Title: Engineered omega-Transaminase Enables Remote Stereocontrol in the Synthesis of Chiral Pharmaceutical N-Heterocyclic Amines with Nonadjacent Stereocenters
Authors: Zhang, Y. / Wang, X. / Yin, X. / Huang, T. / Lin, S.
History
DepositionAug 20, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Omega-Transaminase
D: Omega-Transaminase
F: Omega-Transaminase
H: Omega-Transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,4698
Polymers143,6164
Non-polymers8534
Water21,4381190
1
A: Omega-Transaminase
D: Omega-Transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2344
Polymers71,8082
Non-polymers4272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-25 kcal/mol
Surface area23440 Å2
MethodPISA
2
F: Omega-Transaminase
H: Omega-Transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2344
Polymers71,8082
Non-polymers4272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-25 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.830, 72.450, 84.320
Angle α, β, γ (deg.)74.64, 85.69, 69.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Omega-Transaminase


Mass: 35903.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylobacter lacus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-A1EVZ / ~{tert}-butyl (2~{S})-2-methyl-5-oxidanylidene-piperidine-1-carboxylate


Mass: 213.273 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H19NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1190 / 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: 2.54 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.05M Magnesium chloride hexahydrate, 0.1M MES, 5%w/v PEG4000, 10% 2-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.93→23.39 Å / Num. obs: 102179 / % possible obs: 96.3 % / Redundancy: 3.5 % / CC1/2: 0.982 / Net I/σ(I): 7.2
Reflection shellResolution: 1.93→1.96 Å / Num. unique obs: 5085 / CC1/2: 0.535

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→23.39 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 2000 1.96 %
Rwork0.1876 --
obs0.1883 102160 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.93→23.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9994 0 60 1190 11244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710282
X-RAY DIFFRACTIONf_angle_d0.97513988
X-RAY DIFFRACTIONf_dihedral_angle_d11.9891463
X-RAY DIFFRACTIONf_chiral_restr0.0591527
X-RAY DIFFRACTIONf_plane_restr0.0061819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.26781430.24497142X-RAY DIFFRACTION96
1.98-2.030.31241380.27486944X-RAY DIFFRACTION94
2.03-2.090.29751410.24887067X-RAY DIFFRACTION95
2.09-2.160.22661430.21267131X-RAY DIFFRACTION96
2.16-2.240.2751410.20147113X-RAY DIFFRACTION96
2.24-2.330.24581450.19187231X-RAY DIFFRACTION97
2.33-2.430.23661420.19547138X-RAY DIFFRACTION97
2.43-2.560.23521450.19767232X-RAY DIFFRACTION97
2.56-2.720.24311440.18957217X-RAY DIFFRACTION97
2.72-2.930.21931440.18217211X-RAY DIFFRACTION97
2.93-3.220.2021450.17267248X-RAY DIFFRACTION98
3.22-3.690.18851430.16367163X-RAY DIFFRACTION96
3.69-4.640.17871430.14767150X-RAY DIFFRACTION96
4.64-23.390.19531430.16797173X-RAY DIFFRACTION96

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