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- PDB-7y8o: Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in compl... -

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Basic information

Entry
Database: PDB / ID: 7y8o
TitleStructure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole
ComponentsSciR
KeywordsHYDROLASE/INHIBITOR / substrate binding / HYDROLASE-inhibitor complex
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2-[2,5-bis(fluoranyl)phenyl]pyrrolidine
Function and homology information
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, L.L. / Liu, W.D. / Shi, M. / Huang, J.W. / Yang, Y. / Chen, C.C. / Guo, R.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: to be published
Title: Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(3-fluorophenyl)-3,4-dihydro-2H-pyrrole
Authors: Zhang, L.L. / Liu, W.D. / Shi, M. / Huang, J.W. / Yang, Y. / Chen, C.C. / Guo, R.T.
#1: Journal: Acs Catalysis / Year: 2022
Title: Engineered Imine Reductase for Larotrectinib Intermediate Manufacture
Authors: Chen, Q. / Li, B.B. / Zhang, L. / Chen, X.R. / Zhu, X.X. / Chen, F.F. / Shi, M. / Chen, C.C. / Yang, Y. / Guo, R.T. / Liu, W. / Xu, J.H. / Zheng, G.W.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Apr 3, 2024Group: Database references / Category: citation / Item: _citation.unpublished_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SciR
B: SciR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5055
Polymers60,8352
Non-polymers1,6703
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11360 Å2
ΔGint-99 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.797, 81.358, 93.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SciR


Mass: 30417.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21(DE3)
#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: Chemical ChemComp-Q0R / 2-[2,5-bis(fluoranyl)phenyl]pyrrolidine


Mass: 183.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H11F2N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% Polyethylene glycol 6000, 0.1 M 2-(4-Morpholino) ethanesulfonic acid pH 6.5, 5% 2-methyl-1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jun 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.3→34.7 Å / Num. obs: 43563 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 2186 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQY

4oqy


Resolution: 2.3→34.58 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 2172 4.99 %
Rwork0.186 41332 -
obs0.188 43504 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.07 Å2 / Biso mean: 27.98 Å2 / Biso min: 13.63 Å2
Refinement stepCycle: final / Resolution: 2.3→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 108 357 4681
Biso mean--31.32 30.38 -
Num. residues----573
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.380.27732180.21441474365
2.38-2.480.29712160.216641184334
2.48-2.590.27732150.224641264341
2.59-2.730.32482170.223241404357
2.73-2.90.24632180.221441424360
2.9-3.120.24352200.223341344354
3.12-3.430.2612130.194941514364
3.44-3.930.20972170.16241224339
3.93-4.950.16252240.147841164340
4.95-34.580.17242140.156641364350

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