[English] 日本語
Yorodumi
- EMDB-40947: Closed state of lysine 5,6-aminomutase from Thermoanaerobacter te... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40947
TitleClosed state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Map data
Sample
  • Complex: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
    • Protein or peptide: D-lysine 5,6-aminomutase beta subunit
    • Protein or peptide: D-lysine 5,6-aminomutase alpha subunit
  • Ligand: 5'-DEOXYADENOSINE
  • Ligand: S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine
  • Ligand: COBALAMIN
Keywordslysine 5 / 6-aminomutase / cobalamin / Vitamin B12 / Pyridoxal phosphate / radical / ISOMERASE
Function / homology
Function and homology information


cobalamin binding / catalytic activity / protein dimerization activity / metal ion binding
Similarity search - Function
D-Lysine 5,6-aminomutase alpha subunit / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal / D-lysine 5,6-aminomutase beta subunit KamE, N-terminal domain superfamily / D-Lysine 5,6-aminomutase alpha subunit superfamily / D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit / Dimerisation domain of d-ornithine 4,5-aminomutase / Cobalamin (vitamin B12)-dependent enzyme, catalytic / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain
Similarity search - Domain/homology
D-lysine 5,6-aminomutase beta subunit / D-lysine 5,6-aminomutase alpha subunit
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsTian S / Voss P / Pham K / Klose T / Tjia-Fleck S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Catalysis in Motion: Large-Scale Domain Shift Enables Co-C Bond Homolysis in Lysine 5,6-Aminomutase
Authors: Tian S / Voss P / Pham K / Toba D / Liu M / Das N / Yachuw S / Denault C / Klose T / Uyeda C / Tjia-Fleck S
History
DepositionJun 1, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40947.png

Downloads & links

-
Map

FileDownload / File: emd_40947.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.968 Å		1.08 Å/pix.
x 256 pix.
= 275.968 Å		1.08 Å/pix.
x 256 pix.
= 275.968 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.078 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-1.9133828 - 2.5948935
Average (Standard dev.)-0.0000888442 (±0.047594942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.968 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_40947_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_40947_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

EntireName: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
Components
  • Complex: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
    • Protein or peptide: D-lysine 5,6-aminomutase beta subunit
    • Protein or peptide: D-lysine 5,6-aminomutase alpha subunit
  • Ligand: 5'-DEOXYADENOSINE
  • Ligand: S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine
  • Ligand: COBALAMIN

-
Supramolecule #1: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

SupramoleculeName: Lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)

-
Macromolecule #1: D-lysine 5,6-aminomutase alpha subunit

MacromoleculeName: D-lysine 5,6-aminomutase alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Molecular weightTheoretical: 58.288918 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRESKLNLDW ELVDKAREAA RNIVKDTQKF IDAHTTVSVE RTVCRLLGID GVNDLGVPLP NVVVDHIKSK GNLSLGAATY IGNAMIYTG LSPQEIAERV AKGELDLTSI PMADLFEIKL AVQDIAIKTV EKIRENRRKR EEFLKKYGDK EGPLLYVIVA T GNIYEDVV ...String:
MRESKLNLDW ELVDKAREAA RNIVKDTQKF IDAHTTVSVE RTVCRLLGID GVNDLGVPLP NVVVDHIKSK GNLSLGAATY IGNAMIYTG LSPQEIAERV AKGELDLTSI PMADLFEIKL AVQDIAIKTV EKIRENRRKR EEFLKKYGDK EGPLLYVIVA T GNIYEDVV QAQAAARQGA DVIAVIRATA QSLLDYVPYG PTTEGFGGTY ATQENFRIMR KALDEVSEEL GRYIRLCNYA SG LCMPEIA AMGALERLDV MLNDALYGIL FRDINMKRTM VDQFFSRVIN GFAGIIINTG EDNYLTTADA YEKAHTVLAS QLI NEQFAL IAGIPEEQMG LGHAFEMNPD LRNGFLYELA QAQMVREIFP KAPLKYMPPT KYMTGNIFKG HVQDAMFNVV TIMT KQRIH LLGMLTEAIH TPFMSDRALS IESAKYIFNN MADIADEIYF KEGGIIQRRA NEVLKKAYEL LKEIEQEGLF KALEQ GKFA DIKRPIDGGK GLEGVVEKDP NYFNPFIDLM LRGDRG

UniProtKB: D-lysine 5,6-aminomutase alpha subunit

-
Macromolecule #2: D-lysine 5,6-aminomutase beta subunit

MacromoleculeName: D-lysine 5,6-aminomutase beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Molecular weightTheoretical: 28.643043 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KQYDTTLDLT RVKPYGDTMN DGKVQLSFTL PVPDGAKAVE AAKQLAKKMG LENPMVVYHA PLDKNFTFFI IYGSLIHTVD YTSIQVQEL EIKAMSMEET NEYIKKHIGR KVVVVGATTG TDAHTVGLDA IMNMKGYAGH YGLERYEMIE AYNLGSQVPN E EFVKKAIE ...String:
KQYDTTLDLT RVKPYGDTMN DGKVQLSFTL PVPDGAKAVE AAKQLAKKMG LENPMVVYHA PLDKNFTFFI IYGSLIHTVD YTSIQVQEL EIKAMSMEET NEYIKKHIGR KVVVVGATTG TDAHTVGLDA IMNMKGYAGH YGLERYEMIE AYNLGSQVPN E EFVKKAIE VGADALLVSQ TVTQKDAHIK NLTHLVELLE AEGIRDKVLL ICGGPRITHE LAKELGYDAG FGPGTFADHV AT FIVTEMV KRKIPGLKGY KK

UniProtKB: D-lysine 5,6-aminomutase beta subunit

-
Macromolecule #3: 5'-DEOXYADENOSINE

MacromoleculeName: 5'-DEOXYADENOSINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: 5AD
Molecular weightTheoretical: 251.242 Da
Chemical component information

ChemComp-5AD:
5'-DEOXYADENOSINE

-
Macromolecule #4: S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-...

MacromoleculeName: S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine
type: ligand / ID: 4 / Number of copies: 1 / Formula: X6I
Molecular weightTheoretical: 393.353 Da

-
Macromolecule #5: COBALAMIN

MacromoleculeName: COBALAMIN / type: ligand / ID: 5 / Number of copies: 1 / Formula: B12
Molecular weightTheoretical: 1.330356 KDa
Chemical component information

ChemComp-B12:
COBALAMIN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1.2
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 55.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1xrs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1060403
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-8t0v:
Closed state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more