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- PDB-9g64: F420-dependent oxidoreductase -

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Basic information

Entry
Database: PDB / ID: 9g64
TitleF420-dependent oxidoreductase
ComponentsF420-dependent oxidoreductase
KeywordsBIOSYNTHETIC PROTEIN / F420-dependent reductase / Pepstatin biosynthesis
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMueller, R. / Zhao, H. / Sikandar, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: Tandem ketone reduction in pepstatin biosynthesis reveals an F 420 H 2 -dependent statine pathway.
Authors: Mo, J. / Sikandar, A. / Zhao, H. / Bashiri, G. / Huo, L. / Empting, M. / Muller, R. / Fu, C.
History
DepositionJul 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F420-dependent oxidoreductase
B: F420-dependent oxidoreductase


Theoretical massNumber of molelcules
Total (without water)66,3212
Polymers66,3212
Non-polymers00
Water8,359464
1
A: F420-dependent oxidoreductase


Theoretical massNumber of molelcules
Total (without water)33,1611
Polymers33,1611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F420-dependent oxidoreductase


Theoretical massNumber of molelcules
Total (without water)33,1611
Polymers33,1611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.143, 94.793, 111.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein F420-dependent oxidoreductase / oxidoreductase / kvPepI


Mass: 33160.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) PEG 4000, 0.2 M Sodium acetate and 0.1 M Tris-Cl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.65→48.31 Å / Num. obs: 71666 / % possible obs: 99.6 % / Redundancy: 26.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.4
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 1.75 / Num. unique obs: 3528 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→48.31 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.19 3639 -
Rwork0.17 --
obs-71565 99.35 %
Refinement stepCycle: LAST / Resolution: 1.65→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 0 464 4559
LS refinement shellResolution: 1.65→1.709 Å
RfactorNum. reflection
Rfree0.274 361
Rwork0.241 -
obs-7083

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