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- EMDB-64637: Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64637
TitleCryo-EM structure of E. coli glycine decarboxylase (P-protein) apo
Map dataShanpened map of P protein
Sample
  • Complex: Dimer complex of glycine (de)carboxylating apo open form
    • Protein or peptide: Glycine dehydrogenase (decarboxylating)
Keywords(de)carboxylase / PLP-dependent enzymes / dimer / OXIDOREDUCTASE
Function / homology
Function and homology information


glycine dehydrogenase (aminomethyl-transferring) / glycine dehydrogenase (decarboxylating) activity / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / glycine binding / one-carbon metabolic process / pyridoxal phosphate binding / identical protein binding / cytosol
Similarity search - Function
Glycine dehydrogenase (decarboxylating) / Glycine cleavage system P protein / : / : / Glycine cleavage system P-protein / Glycine dehydrogenase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Glycine dehydrogenase (decarboxylating)
Similarity search - Component
Biological speciesEscherichia coli (strain K12) (bacteria) / Escherichia coli str. K-12 substr. DH10B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.32 Å
AuthorsHan Z / Zeng A
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo
Authors: Han Z / Zeng A
History
DepositionMay 16, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64637.png

Downloads & links

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Map

FileDownload / File: emd_64637.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationShanpened map of P protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 236.6 Å		0.85 Å/pix.
x 280 pix.
= 236.6 Å		0.85 Å/pix.
x 280 pix.
= 236.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.55
Minimum - Maximum-3.2754903 - 5.479713
Average (Standard dev.)-0.00010669233 (±0.15243368)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 236.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unshanpened map of P protein

Fileemd_64637_additional_1.map
AnnotationUnshanpened map of P protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of P protein

Fileemd_64637_half_map_1.map
AnnotationHalf map B of P protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of P protein

Fileemd_64637_half_map_2.map
AnnotationHalf map A of P protein
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer complex of glycine (de)carboxylating apo open form

EntireName: Dimer complex of glycine (de)carboxylating apo open form
Components
  • Complex: Dimer complex of glycine (de)carboxylating apo open form
    • Protein or peptide: Glycine dehydrogenase (decarboxylating)

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Supramolecule #1: Dimer complex of glycine (de)carboxylating apo open form

SupramoleculeName: Dimer complex of glycine (de)carboxylating apo open form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (strain K12) (bacteria)
Molecular weightTheoretical: 104 KDa

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Macromolecule #1: Glycine dehydrogenase (decarboxylating)

MacromoleculeName: Glycine dehydrogenase (decarboxylating) / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: glycine dehydrogenase (aminomethyl-transferring)
Source (natural)Organism: Escherichia coli str. K-12 substr. DH10B (bacteria)
Molecular weightTheoretical: 105.616531 KDa
Recombinant expressionOrganism: Cloning vector pET-28a-ZaTdT12 (others)
SequenceString: MGTQTLSQLE NSGAFIERHI GPDAAQQQEM LNAVGAQSLN ALTGQIVPKD IQLATPPQVG APATEYAALA ELKAIASRNK RFTSYIGMG YTAVQLPPVI LRNMLENPGW YTAYTPYQPE VSQGRLEALL NFQQVTLDLT GLDMASASLL DEATAAAEAM A MAKRVSKL ...String:
MGTQTLSQLE NSGAFIERHI GPDAAQQQEM LNAVGAQSLN ALTGQIVPKD IQLATPPQVG APATEYAALA ELKAIASRNK RFTSYIGMG YTAVQLPPVI LRNMLENPGW YTAYTPYQPE VSQGRLEALL NFQQVTLDLT GLDMASASLL DEATAAAEAM A MAKRVSKL KNANRFFVAS DVHPQTLDVV RTRAETFGFE VIVDDAQKVL DHQDVFGVLL QQVGTTGEIH DYTALISELK SR KIVVSVA ADIMALVLLT APGKQGADIV FGSAQRFGVP MGYGGPHAAF FAAKDEYKRS MPGRIIGVSK DAAGNTALRM AMQ TREQHI RREKANSNIC TSQVLLANIA SLYAVYHGPV GLKRIANRIH RLTDILAAGL QQKGLKLRHA HYFDTLCVEV ADKA GVLTR AEAAEINLRS DILNAVGITL DETTTRENVM QLFNVLLGDN HGLDIDTLDK DVAHDSRSIQ PAMLRDDEIL THPVF NRYH SETEMMRYMH SLERKDLALN QAMIPLGSCT MKLNAAAEMI PITWPEFAEL HPFCPPEQAE GYQQMIAQLA DWLVKL TGY DAVCMQPNSG AQGEYAGLLA IRHYHESRNE GHRDICLIPA SAHGTNPASA HMAGMQVVVV ACDKNGNIDL TDLRAKA EQ AGDNLSCIMV TYPSTHGVYE ETIREVCEVV HQFGGQVYLD GANMNAQVGI TSPGFIGADV SHLNLHKTFC IPHGGGGP G MGPIGVKAHL APFVPGHSVV QIEGMLTRQG AVSAAPFGSA SILPISWMYI RMMGAEGLKK ASQVAILNAN YIASRLQDA FPVLYTGRDG RVAHECILDI RPLKEETGIS ELDIAKRLID YGFHAPTMSF PVAGTLMVEP TESESKVELD RFIDAMLAIR AEIDQVKAG VWPLEDNPLV NAPHIQSELV AEWAHPYSRE VAVFPAGVAD KYWPTVKRLD DVYGDRNLFC SCVPISEYQL E HHHHHH

UniProtKB: Glycine dehydrogenase (decarboxylating)

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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

Concentration1.28 mg/mL
BufferpH: 7.4 / Component - Concentration: 20.0 mg/mL / Component - Formula: Tris-HCl
Component - Name: Tri (Hydroxymethyl) Amino Methane Hydrochloride
Details: pH=7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 287 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeSHUIMU TOTEM 300S
TemperatureMin: 90.0 K / Max: 100.0 K
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 5490 / Average exposure time: 3.29 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 60000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 3153680
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1975829
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Avg.num./class: 626483
Details: The number of particles of each class is 101320, 381526, 1975829, 47258, with a resolution of 6.03, 3.45 ,3.45 and 7.31 angstroms, respectively
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Residue range: 3-952 / Chain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelSMART
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 106.5 / Target criteria: Cross-correlation coefficient
Output model

PDB-9uz6:
Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo

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