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- PDB-9jlk: NADP-dependent oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 9jlk
TitleNADP-dependent oxidoreductase
ComponentsNADP-dependent oxidoreductase
KeywordsBIOSYNTHETIC PROTEIN / alcohol dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
Similarity search - Function
Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsLi, Y. / Zhu, D. / Xie, X. / Li, F. / Lu, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82173702 China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structural Basis for Medium-Chain Dehydrogenase/Reductase-Catalyzed Reductive Cyclization in Polycyclic Tetramate Macrolactam Biosynthesis.
Authors: Xie, X. / Li, F. / Mu, Y. / Lu, M. / Luo, J. / Wang, H. / Shen, Y. / Du, L. / Zhu, D. / Li, Y.
History
DepositionSep 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-dependent oxidoreductase
B: NADP-dependent oxidoreductase


Theoretical massNumber of molelcules
Total (without water)77,8872
Polymers77,8872
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-23 kcal/mol
Surface area29500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.708, 89.708, 203.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein NADP-dependent oxidoreductase / Oxidoreductase / zinc-binding dehydrogenase family protein


Mass: 38943.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Gene: GLE_3219 / Production host: Escherichia coli (E. coli) / References: UniProt: C3PTT2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: PEG3350,sodium chloride,bis-tris hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.33→89.71 Å / Num. obs: 36508 / % possible obs: 100 % / Redundancy: 26 % / CC1/2: 0.999 / Net I/σ(I): 19.3
Reflection shellResolution: 2.33→2.39 Å / Num. unique obs: 2647 / CC1/2: 0.969

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→18.55 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2403 1986 5.48 %
Rwork0.1908 --
obs0.1936 36234 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→18.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 0 114 5586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095600
X-RAY DIFFRACTIONf_angle_d0.9867596
X-RAY DIFFRACTIONf_dihedral_angle_d17.5722034
X-RAY DIFFRACTIONf_chiral_restr0.055826
X-RAY DIFFRACTIONf_plane_restr0.011988
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.390.33731370.252375X-RAY DIFFRACTION100
2.39-2.450.31971410.24942420X-RAY DIFFRACTION100
2.45-2.530.29111380.22822390X-RAY DIFFRACTION100
2.53-2.610.30431400.22662412X-RAY DIFFRACTION100
2.61-2.70.28261400.22352419X-RAY DIFFRACTION100
2.7-2.810.28561410.22082425X-RAY DIFFRACTION100
2.81-2.930.26841400.21092412X-RAY DIFFRACTION100
2.93-3.090.32091410.21732439X-RAY DIFFRACTION100
3.09-3.280.24081400.212426X-RAY DIFFRACTION100
3.28-3.530.25411440.19112458X-RAY DIFFRACTION100
3.53-3.890.20731420.18442463X-RAY DIFFRACTION100
3.89-4.440.22761450.15952482X-RAY DIFFRACTION100
4.44-5.570.21321470.16172530X-RAY DIFFRACTION100
5.57-18.550.20311500.19032597X-RAY DIFFRACTION98

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