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- PDB-9jly: NADP-dependent oxidoreductase complexed with NADP -

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Basic information

Entry
Database: PDB / ID: 9jly
TitleNADP-dependent oxidoreductase complexed with NADP
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: 3.11 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3734
Polymers77,8872
Non-polymers1,4872
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-30 kcal/mol
Surface area28620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.037, 90.037, 203.812
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
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: 2.65 Å3/Da / Density % sol: 53.61 %
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: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.11→50 Å / Num. obs: 15720 / % possible obs: 99.6 % / Redundancy: 12.6 % / Rrim(I) all: 0.193 / Net I/σ(I): 14.9
Reflection shellResolution: 3.11→3.21 Å / Num. unique obs: 2837 / CC1/2: 0.924

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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: 3.11→18 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 1557 10.01 %
Rwork0.1813 --
obs0.1882 15562 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5472 0 96 0 5568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095704
X-RAY DIFFRACTIONf_angle_d1.1177756
X-RAY DIFFRACTIONf_dihedral_angle_d16.3662046
X-RAY DIFFRACTIONf_chiral_restr0.06842
X-RAY DIFFRACTIONf_plane_restr0.009994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.210.3521360.26471213X-RAY DIFFRACTION97
3.21-3.330.27111350.22321232X-RAY DIFFRACTION100
3.33-3.460.27541390.2121249X-RAY DIFFRACTION99
3.46-3.610.31131400.20421258X-RAY DIFFRACTION100
3.61-3.80.27371400.18931252X-RAY DIFFRACTION99
3.8-4.040.25411380.18441252X-RAY DIFFRACTION99
4.04-4.350.24031410.16261269X-RAY DIFFRACTION100
4.35-4.780.2411430.15531287X-RAY DIFFRACTION100
4.78-5.450.23051430.16611285X-RAY DIFFRACTION100
5.45-6.80.26761460.19221318X-RAY DIFFRACTION100
6.8-180.1991560.16241390X-RAY DIFFRACTION99

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