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- EMDB-47366: CryoEM structure of inducible Lysine decarboxylase from Hafnia al... -

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Basic information

Entry
Database: EMDB / ID: EMD-47366
TitleCryoEM structure of inducible Lysine decarboxylase from Hafnia alvei D-hydrazino-Lysine analog at 2.3 Angstrom resolution
Map dataRESOLVE density modified map
Sample
  • Complex: Inducible Lysine decarboxylase from Hafnia alvei with D-alpha-hydrazino-Lysine inhibitor
    • Protein or peptide: Lysine decarboxylase, inducible
  • Ligand: (2R)-6-amino-2-[(2E)-2-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)hydrazin-1-yl]hexanoic acid
  • Ligand: water
KeywordsL-Lysine decarboxylase / cadaverine / D-alpha-hydrazone inhibitor / LYASE
Function / homology
Function and homology information


arginine decarboxylase activity / lysine decarboxylase / L-arginine catabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain ...Orn/Lys/Arg decarboxylase, N-terminal / Ornithine/lysine/arginine decarboxylase / Orn/Lys/Arg decarboxylase, N-terminal domain / Orn/Lys/Arg decarboxylases family 1 pyridoxal-P attachment site. / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal / Orn/Lys/Arg decarboxylase, C-terminal domain superfamily / Orn/Lys/Arg decarboxylase, major domain / Orn/Lys/Arg decarboxylase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
lysine decarboxylase
Similarity search - Component
Biological speciesHafnia alvei ATCC 51873 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsDuhoo Y / Desfosses A / Gutsche I / Doukov TI / Berkowitz DB
Funding support France, United States, 4 items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INBS-0005-02 France
French National Research AgencyANR-17-EURE-0003 France
National Science Foundation (NSF, United States)NSF-2102705 United States
National Science Foundation (NSF, United States)NSF-2400333 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 18, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47366.png

Downloads & links

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Map

FileDownload / File: emd_47366.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRESOLVE density modified map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.15 Å/pix.
x 400 pix.
= 458. Å		1.15 Å/pix.
x 400 pix.
= 458. Å		1.15 Å/pix.
x 400 pix.
= 458. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0641
Minimum - Maximum-1.6729273 - 2.8708928
Average (Standard dev.)-0.0000000000001 (±0.052883454)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 458.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: halfA

Fileemd_47366_half_map_1.map
AnnotationhalfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfB

Fileemd_47366_half_map_2.map
AnnotationhalfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Inducible Lysine decarboxylase from Hafnia alvei with D-alpha-hyd...

EntireName: Inducible Lysine decarboxylase from Hafnia alvei with D-alpha-hydrazino-Lysine inhibitor
Components
  • Complex: Inducible Lysine decarboxylase from Hafnia alvei with D-alpha-hydrazino-Lysine inhibitor
    • Protein or peptide: Lysine decarboxylase, inducible
  • Ligand: (2R)-6-amino-2-[(2E)-2-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)hydrazin-1-yl]hexanoic acid
  • Ligand: water

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Supramolecule #1: Inducible Lysine decarboxylase from Hafnia alvei with D-alpha-hyd...

SupramoleculeName: Inducible Lysine decarboxylase from Hafnia alvei with D-alpha-hydrazino-Lysine inhibitor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Inducible Lysine decarboxylase from Hafnia alvei with D-alpha-hydrazino-Lysine inhibitor in ketoenamine form
Source (natural)Organism: Hafnia alvei ATCC 51873 (bacteria)

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Macromolecule #1: Lysine decarboxylase, inducible

MacromoleculeName: Lysine decarboxylase, inducible / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Hafnia alvei ATCC 51873 (bacteria)
Molecular weightTheoretical: 80.205281 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MNIIAILNHM GVYFKEEPIR ELHKALEALD FQIVYPNDRE DLLKLIDNNA RLCGVIFDWD TYNLDLCEEI SAMNEHLPVY AFANTHSTL DVSLNDLRLN VEFFEYALGA AQDIAQKIRQ STDAYIDEIL PPLTKALFNY VKEGKYTFCT PGHMGGTAFQ K SPVGSIFY ...String:
MNIIAILNHM GVYFKEEPIR ELHKALEALD FQIVYPNDRE DLLKLIDNNA RLCGVIFDWD TYNLDLCEEI SAMNEHLPVY AFANTHSTL DVSLNDLRLN VEFFEYALGA AQDIAQKIRQ STDAYIDEIL PPLTKALFNY VKEGKYTFCT PGHMGGTAFQ K SPVGSIFY DFFGANAMKS DISISVGELG SLLDHSGPHK EAEEYIARTF NAERSYMVTN GTSTANKIVG MYSAPAGSTV LI DRNCHKS LTHLMMMSDI TPIYFRPTRN AYGILGGIPK SEFQHDTIAE RVAQTPNATW PVHAVVTNST YDGLLYNTDY IKE ALDVKS IHFDSAWVPY TNFSPIYKGL CGMSGGRVEG KVIYETQSTH KLLAAFSQAS MIHVKGDINE ETFNEAYMMH TSTS PHYGI VASTETAAAM MKGNAGKRLI NGSIERAIRF RKEIKRLNSE SEGWFFDVWQ PEGIDEAKCW PLDSKDNWHG FKDID NDHM YLDPIKVTLL TPGMQKDGSM ADTGIPASIV SKYLDEHGII VEKTGPYNML FLFSIGIDKT KALSLLRALT DFKRSY DLN LRVKNMLPSL YREDPEFYEN MRIQELAQGI HALIQHHNLP DLMYRAFEVL PTMVMNPHAA FQMELRGQTE EVYLEEM IG KVNANMILPY PPGVPLVMPG EMLTEESRPV LEFLQMLCEI GAHYPGFETD IHGAYRQADG RYTVKVIK

UniProtKB: lysine decarboxylase

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Macromolecule #2: (2R)-6-amino-2-[(2E)-2-({3-hydroxy-2-methyl-5-[(phosphonooxy)meth...

MacromoleculeName: (2R)-6-amino-2-[(2E)-2-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)hydrazin-1-yl]hexanoic acid
type: ligand / ID: 2 / Number of copies: 10 / Formula: A1BD0
Molecular weightTheoretical: 390.329 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 727 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 360000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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