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- PDB-9ji7: NADP-dependent oxidoreductase complexed with NADP and substrate 2 -

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Basic information

Entry
Database: PDB / ID: 9ji7
TitleNADP-dependent oxidoreductase complexed with NADP and substrate 2
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
: / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ox4
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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 11, 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)80,3636
Polymers77,8872
Non-polymers2,4764
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-33 kcal/mol
Surface area27280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.275, 87.275, 226.042
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-A1EBZ / (1Z,3E,5E,7S,8R,9S,10S,11R,13R,15S,16Z,18E,24S)-11-ethyl-2,7-dihydroxy-10-methyl-21,25-diazatetracyclo[22.2.1.08,15.09,13]heptacosa-1,3,5,16,18-pentaene-20,26,27-trione


Mass: 494.622 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H38N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
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: 2.76 Å3/Da / Density % sol: 55.49 %
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 10, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.53→81.42 Å / Num. obs: 30090 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 13.6
Reflection shellResolution: 2.53→2.67 Å / Num. unique obs: 4285 / CC1/2: 0.811

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→59.53 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 2000 6.67 %
Rwork0.1925 --
obs0.1959 29999 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→59.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5568 0 72 148 5788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085782
X-RAY DIFFRACTIONf_angle_d0.9697866
X-RAY DIFFRACTIONf_dihedral_angle_d19.232232
X-RAY DIFFRACTIONf_chiral_restr0.054858
X-RAY DIFFRACTIONf_plane_restr0.0091004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.60.36091390.2681941X-RAY DIFFRACTION100
2.6-2.670.33811390.25231963X-RAY DIFFRACTION100
2.67-2.740.25881420.24281979X-RAY DIFFRACTION100
2.74-2.830.29131390.23611952X-RAY DIFFRACTION100
2.83-2.930.27691400.21941953X-RAY DIFFRACTION100
2.93-3.050.29471410.23971975X-RAY DIFFRACTION100
3.05-3.190.31221400.23931965X-RAY DIFFRACTION100
3.19-3.360.28311430.21562001X-RAY DIFFRACTION100
3.36-3.570.2461410.20221971X-RAY DIFFRACTION100
3.57-3.840.25861430.19032005X-RAY DIFFRACTION100
3.85-4.230.19271430.16431999X-RAY DIFFRACTION100
4.23-4.840.16831450.14342045X-RAY DIFFRACTION100
4.84-6.10.2431470.172057X-RAY DIFFRACTION100
6.1-59.530.21771580.17212193X-RAY DIFFRACTION100

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