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- PDB-7y8l: Structure of ScIRED-R2-V3 from Streptomyces clavuligerus in compl... -

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Entry
Database: PDB / ID: 7y8l
TitleStructure of ScIRED-R2-V3 from Streptomyces clavuligerus in complex with 5-(2,5-difluorophenyl)-3,4-dihydro-2H-pyrrole
Componentsreductase for protein
KeywordsOXIDOREDUCTASE/INHIBITOR / substrate binding / OXIDOREDUCTASE-inhibitor complex
Function / homologyChem-4IS / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-NDP
Function and homology information
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 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
CitationJournal: 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 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: reductase for protein
B: reductase for protein
C: reductase for protein
D: reductase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,79912
Polymers122,0944
Non-polymers3,7048
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27140 Å2
ΔGint-203 kcal/mol
Surface area35130 Å2
2
A: reductase for protein
B: reductase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9006
Polymers61,0472
Non-polymers1,8534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-104 kcal/mol
Surface area19590 Å2
MethodPISA
3
C: reductase for protein
D: reductase for protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8986
Polymers61,0472
Non-polymers1,8514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11880 Å2
ΔGint-100 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.660, 63.151, 134.637
Angle α, β, γ (deg.)90.000, 103.580, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN B
31CHAIN C
41CHAIN D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGPROPROCHAIN AAA3 - 2893 - 289
2ARGARGPROPROCHAIN BBB3 - 2893 - 289
3ARGARGLYSLYSCHAIN CCC3 - 2883 - 288
4PROPROLYSLYSCHAIN DDD4 - 2884 - 288

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Components

#1: Protein
reductase for protein


Mass: 30523.529 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-4IS / 5-[2,5-bis(fluoranyl)phenyl]-3,4-dihydro-2~{H}-pyrrole


Mass: 181.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9F2N / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.19 Å3/Da / Density % sol: 43.94 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% Polyethylene glycol 8000, 0.1 M 2-(4-Morpholino) ethanesulfonic acid pH 6.0, 0.1M Calcium Acetate

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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: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.41→36.42 Å / Num. obs: 40850 / % possible obs: 99.1 % / Redundancy: 6.87 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 8.23
Reflection shellResolution: 2.41→2.51 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.47 / Num. unique obs: 4542 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SAINTdata reduction
Aimless0.6.3data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OQY

4oqy


Resolution: 2.41→36.42 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 3843 5 %
Rwork0.208 72980 -
obs0.211 40815 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.29 Å2 / Biso mean: 43.47 Å2 / Biso min: 16.61 Å2
Refinement stepCycle: final / Resolution: 2.41→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8471 0 244 128 8843
Biso mean--49.67 30 -
Num. residues----1145
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3520X-RAY DIFFRACTIONPOSITIONAL0
12B3520X-RAY DIFFRACTIONPOSITIONAL0
13C3520X-RAY DIFFRACTIONPOSITIONAL0
14D3520X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.41-2.50.33873590.25976888724790
2.5-2.60.34713600.26536998735892
2.6-2.710.30443720.24477128750094
2.71-2.860.3193830.24777343772696
2.86-3.040.32473950.2527399779497
3.04-3.270.30923950.23517427782297
3.27-3.60.26764000.21297444784498
3.6-4.120.22593900.17667402779298
4.12-5.190.21174000.17237492789298
5.19-36.420.24433890.1937459784898

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