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- EMDB-51451: Cryo-EM structure of NMHase in complex with DHU -

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Basic information

Entry
Database: EMDB / ID: EMD-51451
TitleCryo-EM structure of NMHase in complex with DHU
Map dataSharpened map (deepEMhancer) used for modeling
Sample
  • Complex: Complex of NMHase and DHU
    • Other: N-methyl hydantoinase
KeywordsN-methyl hydantoinase Creatine catabolism Dihydrouracil DHU inhibitor / HYDROLASE
Biological speciesGlutamicibacter protophormiae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsClairfeuille T / Rudolph M
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structures of N-methyl hydantoinase reveal large conformational changes during catalysis and a novel prototypic mechanism
Authors: Clairfeuille T / Rudolph M
History
DepositionAug 29, 2024-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51451.png

Downloads & links

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Map

FileDownload / File: emd_51451.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map (deepEMhancer) used for modeling
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 512 pix.
= 335.872 Å		0.66 Å/pix.
x 512 pix.
= 335.872 Å		0.66 Å/pix.
x 512 pix.
= 335.872 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.09155534 - 2.6548634
Average (Standard dev.)0.00077036786 (±0.018014966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 335.872 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51451_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map out of last round of non-uniform refinement

Fileemd_51451_additional_1.map
AnnotationUnsharpened map out of last round of non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A out of last round of non-uniform refinement

Fileemd_51451_half_map_1.map
AnnotationHalf-map A out of last round of non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B out of last round of non-uniform refinement

Fileemd_51451_half_map_2.map
AnnotationHalf-map B out of last round of non-uniform refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of NMHase and DHU

EntireName: Complex of NMHase and DHU
Components
  • Complex: Complex of NMHase and DHU
    • Other: N-methyl hydantoinase

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Supramolecule #1: Complex of NMHase and DHU

SupramoleculeName: Complex of NMHase and DHU / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Glutamicibacter protophormiae (bacteria)

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Macromolecule #1: N-methyl hydantoinase

MacromoleculeName: N-methyl hydantoinase / type: other / ID: 1 / Classification: other
Source (natural)Organism: Glutamicibacter protophormiae (bacteria)
SequenceString: MKRIGVDVGG TFTDLYFSDD DQRIAVVEKV PSTPHDPSEA VINGIKKLCE KAGVSLSEID QLVHGTTVAT NTALTHTGAE VGMITTEGFR DILHIARHKK PHNFSLQQDL PWQTKPLIKR RYRLTVKERI TAPHGEILVP LDEDEVRQRV RELKTAGVQA IAVCLLHSYL ...String:
MKRIGVDVGG TFTDLYFSDD DQRIAVVEKV PSTPHDPSEA VINGIKKLCE KAGVSLSEID QLVHGTTVAT NTALTHTGAE VGMITTEGFR DILHIARHKK PHNFSLQQDL PWQTKPLIKR RYRLTVKERI TAPHGEILVP LDEDEVRQRV RELKTAGVQA IAVCLLHSYL NPEHEQRIGE IVNEEFPEAY LSLSSEIVPL YREYERFSTT ALNAYVGPRV SRYLHRLQEQ AENLGYQREI LLMQSSGGMV PIGEAAKRPV TLMMSGPVGG LIGGMWAAKQ SGFENVVTLD IGGTSADIGV AYQGELRMRH LLDTKIGDHQ AMVPMVDIDT IGAGGGSIAY VDAGGVFRVG PQSAGAVPGP VCYGRGGTEP TSTDAQVLLG RMRPDRILAG SGLDMDLDGA RAAMQGLADK LGMSIEEAAL GALQIQKFGM TQAIEQNSVR RGYDPRDFTL VAAGGAGALF ACEIAAELEV PHVLVPAHPG IIAGIGLLAT DEQYEFVATN RFSFASADAA VIQASYEQLE REANAQLDAE EVPAERRKIV WLADARYEGQ GYEIRFVVPE GPVTTAWLDQ AEAAFHDAHF EEYGHRFKGG TVEVINIRVE ARAVMDELPT PEATQSGSLE NALVETRPVT FQQAGKPVTL DTGFYDRAKM GIGTTFAGPV VIEQYDSTTV IPPGFTGTVD DAGNLVIACP AVTQTVEKLA TPILMRVIGG ALNSAAKEMA SVLFRMSYSS IIRESEDLGA GLFDKDGNVL AESDSTPMFM GSMPKIVKGV ISVLGDDIHD GDVILHNDPY LGATHSPDVA IIEPIFHDGE LVGFAGASGQ LIDNGGAFSG LMVDIQDVQS EGTIFRAVKV YEKGVRQESL IRHILNNTRT PTSNEGDFQA MIAACDLAKS RYLALVERYG RDSVRDAGQF WIDYSERMLR QEIAKIPDGV YETETGYLDD DGRNYGKKLP IVVKVIVEGD EITYDLTGSS EQVPTAYNCA FEGTTVSAFT FITRMMFLDE VAFPVFVPQN EGMLKPLKVI APKGTIFNPN YPAATFSRFS QVQRAVDLAL RALAPVMPER VTAGNSAHIH FMSYSGWDEK QGEYWVYLEV NEGSYGARQD SDGPDSVDNL IANTRNNPIE ELEWRFPMRT DRYELREDPA AAGEYRGGIG IVRENTFLED TAVTCEGERH DSDVPWGAYG GHDGLNASLI KNPGRDGEES WPSKVTGRQL QAGDSLQITV PSGGGFGDPL KRNPLQVLED VLDGFTTTEA ASRDYGVILK TVNGQLTVDL AATAVKRENA VSELSHTN
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.45 mg/mL
BufferpH: 7.4
Details: 20 mM HEPES/NaOH pH 7.4, 100 mM NaCl, 100 mM MgCl2, 30 mM NH4Cl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 301 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7046 / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 80000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.4) / Number images used: 430323
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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