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- PDB-9jm9: NADP-dependent oxidoreductase complexed with NADP and substrate 3 -

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Basic information

Entry
Database: PDB / ID: 9jm9
TitleNADP-dependent oxidoreductase complexed with NADP and substrate 3
ComponentsNADP-dependent oxidoreductase
KeywordsBIOSYNTHETIC PROTEIN / alcohol dehydrogenase / complex
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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ox4
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 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 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,8505
Polymers77,8872
Non-polymers1,9633
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-34 kcal/mol
Surface area28180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.790, 87.790, 219.611
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: 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-A1EDR / (1Z,3E,5E,7R,8S,10R,11R,12S,15S,16E,18E,25S)-11-ethyl-2-hydroxy-10-methyl-21,26-diazatetracyclo[23.2.1.07,15.08,12]octacosa-1,3,5,13,16,18-hexaene-20,27,28-trione


Mass: 476.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N2O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350,sodium chloride,bis-tris hydrochloride / PH range: 8.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2022
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.38→81.52 Å / Num. obs: 12784 / % possible obs: 100 % / Redundancy: 12.3 % / CC1/2: 0.996 / Net I/σ(I): 10.1
Reflection shellResolution: 3.38→3.56 Å / Num. unique obs: 1798 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
HKL-3000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.38→62.08 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2848 637 5.01 %
Rwork0.201 --
obs0.2051 12718 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.38→62.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 131 0 5603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095742
X-RAY DIFFRACTIONf_angle_d1.1627809
X-RAY DIFFRACTIONf_dihedral_angle_d16.5482200
X-RAY DIFFRACTIONf_chiral_restr0.061849
X-RAY DIFFRACTIONf_plane_restr0.009999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.38-3.640.33941230.2482343X-RAY DIFFRACTION100
3.64-40.29181250.23772371X-RAY DIFFRACTION100
4-4.580.28561250.17922371X-RAY DIFFRACTION100
4.58-5.770.27011280.19842425X-RAY DIFFRACTION100
5.78-62.080.27441360.18622571X-RAY DIFFRACTION100

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