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- PDB-9j0e: A Chemoenzymatic Strategy for Efficient Synthesis of Aporphine Al... -

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Basic information

Entry
Database: PDB / ID: 9j0e
TitleA Chemoenzymatic Strategy for Efficient Synthesis of Aporphine Alkaloids
ComponentsPutative oxidoreductase GLYR1 like protein
KeywordsOXIDOREDUCTASE / Imine Reductase / alkaloid
Function / homology
Function and homology information


NADP binding / oxidoreductase activity
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / 6-phosphogluconate dehydrogenase, domain 2 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative oxidoreductase GLYR1 like protein
Similarity search - Component
Biological speciesStreptomyces aurantiacus JA 4570 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsYang, L. / Qu, X.D.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22XD1421300 China
National Natural Science Foundation of China (NSFC)23ZR1432800 China
CitationJournal: To Be Published
Title: Catalyst-free photoinitiated intramolecular carbon-carbon coupling enables the efficient synthesis of pharmaceutically important biaryls
Authors: Yang, L. / Qu, X.D.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase GLYR1 like protein
B: Putative oxidoreductase GLYR1 like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3264
Polymers59,8402
Non-polymers1,4872
Water15,259847
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-89 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.490, 133.760, 43.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-759-

HOH

21A-890-

HOH

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Components

#1: Protein Putative oxidoreductase GLYR1 like protein


Mass: 29919.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces aurantiacus JA 4570 (bacteria)
Gene: STRAU_4331 / Production host: Escherichia coli (E. coli) / References: UniProt: S3ZG23
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: sodium acetate, ammonium sulfate, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.46→44.59 Å / Num. obs: 103714 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Net I/σ(I): 13.4
Reflection shellResolution: 1.46→1.5 Å / Num. unique obs: 7593 / CC1/2: 0.842

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→40.82 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1911 1999 1.93 %
Rwork0.1746 --
obs0.175 103614 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.46→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4201 0 96 847 5144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054383
X-RAY DIFFRACTIONf_angle_d0.7995990
X-RAY DIFFRACTIONf_dihedral_angle_d18.7211632
X-RAY DIFFRACTIONf_chiral_restr0.07694
X-RAY DIFFRACTIONf_plane_restr0.008773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.2641410.25947164X-RAY DIFFRACTION100
1.5-1.540.25811410.23847174X-RAY DIFFRACTION100
1.54-1.580.24751400.21577143X-RAY DIFFRACTION100
1.58-1.630.23191430.20077199X-RAY DIFFRACTION100
1.63-1.690.18961410.19527191X-RAY DIFFRACTION100
1.69-1.760.23041410.19487181X-RAY DIFFRACTION100
1.76-1.840.19231420.18497199X-RAY DIFFRACTION100
1.84-1.940.19781420.17487217X-RAY DIFFRACTION100
1.94-2.060.17641430.17037252X-RAY DIFFRACTION100
2.06-2.220.20081420.16517234X-RAY DIFFRACTION100
2.22-2.440.19731440.16597293X-RAY DIFFRACTION100
2.44-2.790.18671440.17367308X-RAY DIFFRACTION100
2.79-3.520.16191450.16517395X-RAY DIFFRACTION100
3.52-40.820.17861500.15717665X-RAY DIFFRACTION100

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