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- PDB-9h03: NMHase, dihydrouridine, 2.1A, CC_mask=0.7859 -

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Basic information

Entry
Database: PDB / ID: 9h03
TitleNMHase, dihydrouridine, 2.1A, CC_mask=0.7859
ComponentsN-Methylhydantoinase
KeywordsHYDROLASE / ATPASE / NMH / DHU / ATP-BINDING / CREATINE METABOLISM / HYDROLASE 1
Function / homologyDIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE
Function and homology information
Biological speciesGlutamicibacter protophormiae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsToedtli, P. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To Be Published
Title: NMHase, dihydrouridine, 2.1A, CC_mask=0.7859
Authors: Toedtli, P. / Rudolph, M.G.
History
DepositionOct 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 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: N-Methylhydantoinase
B: N-Methylhydantoinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,5576
Polymers280,2482
Non-polymers3084
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, from map, used C2 as constraint, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein N-Methylhydantoinase


Mass: 140124.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glutamicibacter protophormiae (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DUC / DIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE / DIHYDROURACIL


Mass: 114.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NMHase-DHU complex / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Glutamicibacter protophormiae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 0.45 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / C2 aperture diameter: 30 µm
Image recordingAverage exposure time: 1.2 sec. / Electron dose: 39 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7046

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 430323 / Symmetry type: POINT

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