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- EMDB-63940: Tetrameric cystathionine beta-synthase of Mycobacterium tuberculo... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-63940
TitleTetrameric cystathionine beta-synthase of Mycobacterium tuberculosis bound to O-Benzylhydroxylamine
Map dataPhCH2ONH2-bound MtbCBS map
Sample
  • Complex: The ternary complex of O-Benzylhydroxylamine bound to MtbCBS
    • Protein or peptide: Probable cystathionine beta-synthase Rv1077
  • Ligand: O-benzylhydroxylamine
KeywordsInhibitor / Lyase / Complex
Function / homology
Function and homology information


cystathionine beta-synthase / cystathionine beta-synthase activity / : / cysteine synthase activity / : / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Cystathionine beta-synthase, C-terminal domain / Cystathionine beta-synthase / : / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Probable cystathionine beta-synthase Rv1077
Similarity search - Component
Biological speciesMycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) / Mycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsPolepalli S / Roy A / Mondal B / Dutta S
Funding support India, 2 items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)(BT/INF/22/SP22844/2017) India
Department of Science & Technology (DST, India)(SR/FST/LSII-039/2015) India
CitationJournal: To Be Published
Title: Tetrameric cystathionine beta-synthase of Mycobacterium tuberculosis bound to O-Benzylhydroxylamine
Authors: Polepalli S / Roy A / Mondal B / Dutta S
History
DepositionMar 25, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63940.png

Downloads & links

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Map

FileDownload / File: emd_63940.map.gz / Format: CCP4 / Size: 95 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhCH2ONH2-bound MtbCBS map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 292 pix.
= 268.64 Å		0.92 Å/pix.
x 292 pix.
= 268.64 Å		0.92 Å/pix.
x 292 pix.
= 268.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.103
Minimum - Maximum-0.48976973 - 0.72426915
Average (Standard dev.)0.00026747482 (±0.023685096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions292292292
Spacing292292292
CellA=B=C: 268.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: PhCH2ONH2-bound MtbCBS half-map B

Fileemd_63940_half_map_1.map
AnnotationPhCH2ONH2-bound MtbCBS half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: PhCH2ONH2-bound MtbCBS half-map A

Fileemd_63940_half_map_2.map
AnnotationPhCH2ONH2-bound MtbCBS half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The ternary complex of O-Benzylhydroxylamine bound to MtbCBS

EntireName: The ternary complex of O-Benzylhydroxylamine bound to MtbCBS
Components
  • Complex: The ternary complex of O-Benzylhydroxylamine bound to MtbCBS
    • Protein or peptide: Probable cystathionine beta-synthase Rv1077
  • Ligand: O-benzylhydroxylamine

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Supramolecule #1: The ternary complex of O-Benzylhydroxylamine bound to MtbCBS

SupramoleculeName: The ternary complex of O-Benzylhydroxylamine bound to MtbCBS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)

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Macromolecule #1: Probable cystathionine beta-synthase Rv1077

MacromoleculeName: Probable cystathionine beta-synthase Rv1077 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: cystathionine beta-synthase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 50.512969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MARIAQHISE LIGGTPLVRL NSVVPDGAGT VAAKVEYLNP GGSS(LLP)DRIAV KMIEAAEASG QLKPGGTIVE PTSGNT GVG LALVAQRRGY KCVFVCPDKV SEDKRNVLIA YGAEVVVCPT AVPPHDPASY YSVSDRLVRD IDGAWKPDQY ANPEGPA SH YVTTGPEIWA ...String:
MARIAQHISE LIGGTPLVRL NSVVPDGAGT VAAKVEYLNP GGSS(LLP)DRIAV KMIEAAEASG QLKPGGTIVE PTSGNT GVG LALVAQRRGY KCVFVCPDKV SEDKRNVLIA YGAEVVVCPT AVPPHDPASY YSVSDRLVRD IDGAWKPDQY ANPEGPA SH YVTTGPEIWA DTEGKVTHFV AGIGTGGTIT GAGRYLKEVS GGRVRIVGAD PEGSVYSGGA GRPYLVEGVG EDFWPAAY D PSVPDEIIAV SDSDSFDMTR RLAREEAMLV GGSCGMAVVA ALKVAEEAGP DALIVVLLPD GGRGYMSKIF NDAWMSSYG FLRSRLDGST EQSTVGDVLR RKSGALPALV HTHPSETVRD AIGILREYGV SQMPVVGAEP PVMAGEVAGS VSERELLSAV FEGRAKLAD AVSAHMSPPL RMIGAGELVS AAGKALRDWD ALMVVEEGKP VGVITRYDLL GFLSEGAGRR KLAAALEHHH H HH

UniProtKB: Probable cystathionine beta-synthase Rv1077

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Macromolecule #2: O-benzylhydroxylamine

MacromoleculeName: O-benzylhydroxylamine / type: ligand / ID: 2 / Number of copies: 4 / Formula: OBZ
Molecular weightTheoretical: 123.152 Da
Chemical component information

ChemComp-OBZ:
O-benzylhydroxylamine

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211131
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION

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