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- PDB-9jp8: NADP-dependent oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 9jp8
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
Unknown ligand / NADP-dependent oxidoreductase
Similarity search - Component
Biological speciesKitasatospora sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 25, 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
C: NADP-dependent oxidoreductase
D: NADP-dependent oxidoreductase
E: NADP-dependent oxidoreductase
F: NADP-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,62324
Polymers233,9176
Non-polymers1,70518
Water19,5281084
1
A: NADP-dependent oxidoreductase
B: NADP-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6379
Polymers77,9722
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-100 kcal/mol
Surface area29200 Å2
MethodPISA
2
C: NADP-dependent oxidoreductase
D: NADP-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5418
Polymers77,9722
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-94 kcal/mol
Surface area28960 Å2
MethodPISA
3
E: NADP-dependent oxidoreductase
F: NADP-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4457
Polymers77,9722
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-73 kcal/mol
Surface area29130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.734, 115.734, 158.271
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
NADP-dependent oxidoreductase


Mass: 38986.234 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora sp. (bacteria) / Gene: cftD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8F0WPM9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1084 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl, ammonium sulfate

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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: 2→50 Å / Num. obs: 159605 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.998 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 15908 / CC1/2: 0.941

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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→25.53 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 2020 1.27 %
Rwork0.202 --
obs0.2026 159255 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→25.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16482 0 96 1084 17662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716962
X-RAY DIFFRACTIONf_angle_d0.84623082
X-RAY DIFFRACTIONf_dihedral_angle_d17.5776102
X-RAY DIFFRACTIONf_chiral_restr0.0572532
X-RAY DIFFRACTIONf_plane_restr0.0073000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.27951420.242911098X-RAY DIFFRACTION99
2.05-2.110.30231400.224811352X-RAY DIFFRACTION100
2.11-2.170.27661480.209911139X-RAY DIFFRACTION100
2.17-2.240.38361470.249911183X-RAY DIFFRACTION99
2.24-2.320.37671320.321911205X-RAY DIFFRACTION99
2.32-2.410.27331520.226411272X-RAY DIFFRACTION100
2.41-2.520.31291420.222911194X-RAY DIFFRACTION100
2.52-2.660.28651450.247411280X-RAY DIFFRACTION100
2.66-2.820.26541380.247411227X-RAY DIFFRACTION100
2.82-3.040.27611520.226511287X-RAY DIFFRACTION100
3.04-3.340.25681380.207311243X-RAY DIFFRACTION100
3.34-3.830.20091440.186411255X-RAY DIFFRACTION100
3.83-4.820.20061440.158811280X-RAY DIFFRACTION100
4.82-25.530.21761560.168711220X-RAY DIFFRACTION100

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