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- PDB-7y8n: Structure of ScIRED-R3-V4 from Streptomyces clavuligerus in compl... -

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Basic information

Entry
Database: PDB / ID: 7y8n
TitleStructure of ScIRED-R3-V4 from Streptomyces clavuligerus in complex with 5-(2,5-difluorophenyl)-3,4-dihydro-2H-pyrrole
ComponentsBeta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE/INHIBITOR / substrate binding / OXIDOREDUCTASE-inhibitor complex
Function / homologyChem-4IS / Chem-NDP
Function and homology information
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
B: Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5075
Polymers60,8352
Non-polymers1,6723
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-97 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.531, 80.988, 93.028
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 Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase


Mass: 30417.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET32Xa/LIC / 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.: 2 / 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.: 1 / Source method: obtained synthetically / Formula: C10H9F2N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Ammonium Acetate,Sodium Acetate trihydrate,Polyethylene Glycol 4000, Glycerol

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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: Jul 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.2→37.13 Å / Num. obs: 49197 / % possible obs: 99.7 % / Redundancy: 4.85 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.038 / Rrim(I) all: 0.085 / Net I/σ(I): 13.18
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.29 % / Rmerge(I) obs: 0.204 / Num. unique obs: 3164 / CC1/2: 0.969 / % possible all: 98.8

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Processing

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

4oqy


Resolution: 2.2→37.13 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2094 2470 5.03 %
Rwork0.1745 46659 -
obs0.1763 49129 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.81 Å2 / Biso mean: 23.8135 Å2 / Biso min: 9.86 Å2
Refinement stepCycle: final / Resolution: 2.2→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4222 0 109 448 4779
Biso mean--25.81 28.67 -
Num. residues----574
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 (%)
2.2-2.280.24762420.20124590483298
2.28-2.370.24172430.190347044947100
2.37-2.480.26152480.195146594907100
2.48-2.610.23122380.192746934931100
2.61-2.770.23992510.196146594910100
2.77-2.990.22962480.198946924940100
2.99-3.290.18732470.186846654912100
3.29-3.760.20452550.16146554910100
3.76-4.740.17692490.142346954944100
4.74-37.130.18552490.15894647489699

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