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- EMDB-40947: Closed state of lysine 5,6-aminomutase from Thermoanaerobacter te... -

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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: COBALAMIN
  • Ligand: 5'-DEOXYADENOSINE
  • Ligand: S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine
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
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
History
DepositionJun 1, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40947.png

Downloads & links

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Map

FileDownload / File: emd_40947.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.078 Å
Density
Contour LevelBy AUTHOR: 0.2
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 °

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Supplemental data

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Half map: #2

Fileemd_40947_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40947_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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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: COBALAMIN
  • Ligand: 5'-DEOXYADENOSINE
  • Ligand: S-{2-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]ethyl}-L-cysteine

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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: #1-#2
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)

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

MacromoleculeName: D-lysine 5,6-aminomutase beta subunit / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Molecular weightTheoretical: 29.72825 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSSGLYSTEK KQYDTTLDLT RVKPYGDTMN DGKVQLSFTL PVPDGAKAVE AAKQLAKKMG LENPMVVYHA PLDKNFTFFI IYGSLIHTV DYTSIQVQEL EIKAMSMEET NEYIKKHIGR KVVVVGATTG TDAHTVGLDA IMNMKGYAGH YGLERYEMIE A YNLGSQVP ...String:
MSSGLYSTEK KQYDTTLDLT RVKPYGDTMN DGKVQLSFTL PVPDGAKAVE AAKQLAKKMG LENPMVVYHA PLDKNFTFFI IYGSLIHTV DYTSIQVQEL EIKAMSMEET NEYIKKHIGR KVVVVGATTG TDAHTVGLDA IMNMKGYAGH YGLERYEMIE A YNLGSQVP NEEFVKKAIE VGADALLVSQ TVTQKDAHIK NLTHLVELLE AEGIRDKVLL ICGGPRITHE LAKELGYDAG FG PGTFADH VATFIVTEMV KRKIPGLKGY KK

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

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

MacromoleculeName: D-lysine 5,6-aminomutase alpha subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
Molecular weightTheoretical: 59.695445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQMRESKLNL DWELVDKARE AARNIVKDTQ KFIDAHTTVS VERTVCRLLG IDGVNDLGVP LPNVVVDHIK SKGNLSLGA ATYIGNAMIY TGLSPQEIAE RVAKGELDLT SIPMADLFEI KLAVQDIAIK TVEKIRENRR KREEFLKKYG D KEGPLLYV ...String:
MGSSHHHHHH SQMRESKLNL DWELVDKARE AARNIVKDTQ KFIDAHTTVS VERTVCRLLG IDGVNDLGVP LPNVVVDHIK SKGNLSLGA ATYIGNAMIY TGLSPQEIAE RVAKGELDLT SIPMADLFEI KLAVQDIAIK TVEKIRENRR KREEFLKKYG D KEGPLLYV IVATGNIYED VVQAQAAARQ GADVIAVIRA TAQSLLDYVP YGPTTEGFGG TYATQENFRI MRKALDEVSE EL GRYIRLC NYASGLCMPE IAAMGALERL DVMLNDALYG ILFRDINMKR TMVDQFFSRV INGFAGIIIN TGEDNYLTTA DAY EKAHTV LASQLINEQF ALIAGIPEEQ MGLGHAFEMN PDLRNGFLYE LAQAQMVREI FPKAPLKYMP PTKYMTGNIF KGHV QDAMF NVVTIMTKQR IHLLGMLTEA IHTPFMSDRA LSIESAKYIF NNMADIADEI YFKEGGIIQR RANEVLKKAY ELLKE IEQE GLFKALEQGK FADIKRPIDG GKGLEGVVEK DPNYFNPFID LMLRGDRG

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

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Macromolecule #3: COBALAMIN

MacromoleculeName: COBALAMIN / type: ligand / ID: 3 / Number of copies: 1 / Formula: B12
Molecular weightTheoretical: 1.330356 KDa
Chemical component information

ChemComp-B12:
COBALAMIN

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Macromolecule #4: 5'-DEOXYADENOSINE

MacromoleculeName: 5'-DEOXYADENOSINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: 5AD
Molecular weightTheoretical: 251.242 Da
Chemical component information

ChemComp-5AD:
5'-DEOXYADENOSINE

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Macromolecule #5: 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: 5 / Number of copies: 1 / Formula: X6I
Molecular weightTheoretical: 393.353 Da

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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

Concentration1.5 mg/mL
BufferpH: 8.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN 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

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Image processing

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 / Number images used: 1060403
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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