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- PDB-7y8k: Structure of ScIRED wild-type from Streptomyces clavuligerus -

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Basic information

Entry
Database: PDB / ID: 7y8k
TitleStructure of ScIRED wild-type from Streptomyces clavuligerus
ComponentsBeta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
KeywordsHYDROLASE / substrate binding
Function / homology
Function and homology information


organic acid catabolic process / 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 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 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 1.0Mar 22, 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: Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase
B: Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)60,9372
Polymers60,9372
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-92 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.195, 63.731, 162.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-408-

HOH

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Components

#1: Protein Beta-hydroxyacid dehydrogenase, 3-hydroxyisobutyrate dehydrogenase


Mass: 30468.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_2776 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E2PUR9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.11 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
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: Jun 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.08→38.44 Å / Num. obs: 57293 / % possible obs: 99.7 % / Redundancy: 7.69 % / Biso Wilson estimate: 23.28 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 8.25
Reflection shellResolution: 2.08→2.18 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 2112 / % possible all: 99.4

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Processing

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

4oqy


Resolution: 2.08→38.44 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 2839 4.96 %
Rwork0.204 54392 -
obs0.206 57231 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.55 Å2 / Biso mean: 28.45 Å2 / Biso min: 9.81 Å2
Refinement stepCycle: final / Resolution: 2.08→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4211 0 0 317 4528
Biso mean---31.27 -
Num. residues----571
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 (%)
2.08-2.150.30932710.28225189546094
2.15-2.240.30322760.25835287556396
2.24-2.340.2922750.25685315559096
2.34-2.470.33822870.24565477576498
2.47-2.620.26972870.22825492577999
2.62-2.820.28452900.215755415831100
2.82-3.110.29452900.204454955785100
3.11-3.560.21552860.187755665852100
3.56-4.480.22392850.158255365821100
4.48-38.440.19992920.18115494578699

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