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- EMDB-36851: Cryo-EM structure of PseP with NAD at 2.86 angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-36851
TitleCryo-EM structure of PseP with NAD at 2.86 angstrom resolution
Map data
Sample
  • Complex: PseP
    • Protein or peptide: PseP
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Keywordsaltemicidin / pyridoxal 5'-phosphate / PLP-dependent enzyme / LYASE
Biological speciesPseudomonas fluorescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsMori T / Awakawa T / Adachi N / Abe I
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121001 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of PseP with NAD at 2.86 angstrom resolution
Authors: Mori T / Awakawa T / Adachi N / Abe I
History
DepositionJul 15, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36851.png

Downloads & links

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Map

FileDownload / File: emd_36851.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.109306835 - 0.1825267
Average (Standard dev.)0.00008222978 (±0.00507058)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36851_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36851_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36851_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PseP

EntireName: PseP
Components
  • Complex: PseP
    • Protein or peptide: PseP
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

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Supramolecule #1: PseP

SupramoleculeName: PseP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: PLP-dependent enzyme in the biosynthesis of altemicidin
Source (natural)Organism: Pseudomonas fluorescens (bacteria)
Molecular weightTheoretical: 90 KDa

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Macromolecule #1: PseP

MacromoleculeName: PseP / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas fluorescens (bacteria)
Molecular weightTheoretical: 90.951523 KDa
Recombinant expressionOrganism: Streptomyces lividans TK24 (bacteria)
SequenceString: VNGTFVESIA DAHVELRAAM LGSRHHPSPD IPIINHPSAS GLDQAFALVE ASLTAHGLAI VQMDEPLSTE QFACYARRLG VLVPEHDED VQPFVEQGDI LHLRTRFGPT DRVGLQPFSS SPLSMHSESS GNALVDQPRY LAFQCLEPGE FAYAPQTLLI D MASIVARI ...String:
VNGTFVESIA DAHVELRAAM LGSRHHPSPD IPIINHPSAS GLDQAFALVE ASLTAHGLAI VQMDEPLSTE QFACYARRLG VLVPEHDED VQPFVEQGDI LHLRTRFGPT DRVGLQPFSS SPLSMHSESS GNALVDQPRY LAFQCLEPGE FAYAPQTLLI D MASIVARI SPYNINILAR TYYDSQRNSP PLLRYDGQRW VISFRDFQQQ PLSWVHEGPT PAGDVLSAIR DLLACMYTAQ AS AVRWARG MFMVFDNQRY MHARSKGHFV LDQQDRHLLR ARIRARTPDL NVLAAVDDGD SRVLFARPAS GRIPQLPDDF RQT SAVEPN QVEETPDTFI DERTLEVFSR ALNPTNPMEL RNLWLGRVEA ELGDNALRPE YADLWRRSRV RRAVSVEEVL RSTA TVGMV KELFNAFFRD DLYGALSSKR NIILSSGAVD EDEYGLPAAL KETLRFALAR NFYGYSDSLG RQPAREAVAA MESVS MQQG HYEAASVALT MGATHTISSL ADFIFRDNPY ADAAICAIPN YPPLVQSIAW RHPVLLVPTP SHGGTTSLQA LSRAVT PNT PMVLLQTGTN PCGSLVDELE LERFIQSTSL STLIILDECH EWLGAPRHFS PARQRANVIR VSSLS(LLP)NWSV PGL KVGWFL ADPALVSRYY EFASTSYGGP QSFVYTLVEV LARFERWIIE GRTSIDQQQL REFSASYGLQ LGSLSQTYEH YVAE RRARE QVLLGLRGEA TSCLRRASMI VKTPQCSINV FAQIPGSEDS YLSFRNVLRE TGVSVYPGIL SFYLAGGGFR VTTAR KWGD LHRGLERLSA GAGNA

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 2 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

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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

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was mono-disperse.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3006 / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2478450
Startup modelType of model: OTHER
Details: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 30 A for use as an initial model for 3D classification.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 462772
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationNumber classes: 1 / Avg.num./class: 462772 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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