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Yorodumi- EMDB-17324: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17324 | |||||||||
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Title | Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with product, benzoyl-CoA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | prFMN / plastic degradation / Phthalates / anaerobic / light sensitive / Co-enzyme A / decarboxylase / benzoyl CoA / product bound / FLAVOPROTEIN | |||||||||
Biological species | Thauera chlorobenzoica (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.3 Å | |||||||||
Authors | Kayastha K / Ermler U | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Phthaloyl-CoA decarboxylase (Pcd) bound with product, benzoyl-CoA Authors: Kayastha K / Ermler U | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17324.map.gz | 97.5 MB | EMDB map data format | |
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Header (meta data) | emd-17324-v30.xml emd-17324.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17324_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_17324.png | 172.6 KB | ||
Filedesc metadata | emd-17324.cif.gz | 6.1 KB | ||
Others | emd_17324_half_map_1.map.gz emd_17324_half_map_2.map.gz | 98.3 MB 98.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17324 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17324 | HTTPS FTP |
-Validation report
Summary document | emd_17324_validation.pdf.gz | 740.5 KB | Display | EMDB validaton report |
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Full document | emd_17324_full_validation.pdf.gz | 740.1 KB | Display | |
Data in XML | emd_17324_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | emd_17324_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17324 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17324 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17324.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_17324_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_17324_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Phthaloyl-CoA decarboxylase (Pcd) bound with benzoyl-CoA
Entire | Name: Phthaloyl-CoA decarboxylase (Pcd) bound with benzoyl-CoA |
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Components |
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-Supramolecule #1: Phthaloyl-CoA decarboxylase (Pcd) bound with benzoyl-CoA
Supramolecule | Name: Phthaloyl-CoA decarboxylase (Pcd) bound with benzoyl-CoA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Thauera chlorobenzoica (bacteria) |
Molecular weight | Theoretical: 360 KDa |
-Macromolecule #1: Phthaloyl-CoA decarboxylase (Pcd)
Macromolecule | Name: Phthaloyl-CoA decarboxylase (Pcd) / type: protein_or_peptide / ID: 1 Details: Pcd monomers bound with co-factors prFMN, Fe, K and reaction product, Benzoyl-CoA. Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Thauera chlorobenzoica (bacteria) |
Molecular weight | Theoretical: 57.682492 KDa |
Sequence | String: ERVGEKDLRA ALEWFRSKGY LVETNKEVNP DLEITGLQKI FDGSLPMLFN NVKDMPHARA ITNLFGDIRV VEELFGWENS LDRVKKVAR AIDHPLKPVI IGQDEAPVQE EVLTTDLDVN KWLTAIRHTP LETEMTIGSG ISCVVGPYFD GGSHIGYNRM N FRWGNVGT ...String: ERVGEKDLRA ALEWFRSKGY LVETNKEVNP DLEITGLQKI FDGSLPMLFN NVKDMPHARA ITNLFGDIRV VEELFGWENS LDRVKKVAR AIDHPLKPVI IGQDEAPVQE EVLTTDLDVN KWLTAIRHTP LETEMTIGSG ISCVVGPYFD GGSHIGYNRM N FRWGNVGT FQISPGSHMW QVMTEHYKDD EPIPLTMCFG VPPSCTYVAG AGFDYAILPK GCDEIGIAGA IQGSPVRLVK CR TIDAYTL ADAEYVLEGY LHPRDKRYET AESEAADIQG RFHFHPEWAG YMGKAYKAPT FHVTAITMRR RESKPIIFPL GVH TADDAN IDTSVRESAI FALCERLQPG IVQNVHIPYC MTDWGGCIIQ VKKRNQIEEG WQRNFLAAIL ACSQGMRLAI AVSE DVDIY SMDDIMWCLT TRVNPQTDIL NPLPGGRGQT FMPAERMTSG DKQWTASNTQ FEGGMGIDAT VPYGYESDFH RPVYG VDLV KPENFFDAKD IDKMKSRMAG WVLSLARTGR |
-Macromolecule #2: benzoyl coenzyme A
Macromolecule | Name: benzoyl coenzyme A / type: ligand / ID: 2 / Number of copies: 6 / Formula: BYC |
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Molecular weight | Theoretical: 871.64 Da |
Chemical component information | ChemComp-BYC: |
-Macromolecule #3: hydroxylated prenyl-FMN
Macromolecule | Name: hydroxylated prenyl-FMN / type: ligand / ID: 3 / Number of copies: 6 / Formula: BYN |
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Molecular weight | Theoretical: 542.476 Da |
Chemical component information | ChemComp-BYN: |
-Macromolecule #4: FE (III) ION
Macromolecule | Name: FE (III) ION / type: ligand / ID: 4 / Number of copies: 12 / Formula: FE |
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Molecular weight | Theoretical: 55.845 Da |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 6 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #6: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 59 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 135 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 30 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6743 / Average exposure time: 3.38 sec. / Average electron dose: 52.27 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: experimental model / Details: pdb from the first holo-complex was used |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-8p02: |