+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60397 | |||||||||
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Title | EcGK filament at APO state. (CASP target) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transferase / Proline biosynthesis / amino acid kinase | |||||||||
Function / homology | Function and homology information proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding ...proline binding / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / phosphorylation / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.67 Å | |||||||||
Authors | Zhang T / Leng Q / Liu LJ | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: EcGPR tetramer with catalytic intermediates Authors: Zhang T / Leng Q / Liu LJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60397.map.gz | 31.9 MB | EMDB map data format | |
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Header (meta data) | emd-60397-v30.xml emd-60397.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_60397_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_60397.png | 99.4 KB | ||
Filedesc metadata | emd-60397.cif.gz | 5.3 KB | ||
Others | emd_60397_additional_1.map.gz emd_60397_half_map_1.map.gz emd_60397_half_map_2.map.gz | 7.8 MB 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60397 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60397 | HTTPS FTP |
-Validation report
Summary document | emd_60397_validation.pdf.gz | 933.9 KB | Display | EMDB validaton report |
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Full document | emd_60397_full_validation.pdf.gz | 933.5 KB | Display | |
Data in XML | emd_60397_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_60397_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60397 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60397 | HTTPS FTP |
-Related structure data
Related structure data | 8zriMC 8zpjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_60397.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Local filtered map
File | emd_60397_additional_1.map | ||||||||||||
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Annotation | Local filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_60397_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60397_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : EcGK at APO state.
Entire | Name: EcGK at APO state. |
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Components |
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-Supramolecule #1: EcGK at APO state.
Supramolecule | Name: EcGK at APO state. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
-Macromolecule #1: Glutamate 5-kinase
Macromolecule | Name: Glutamate 5-kinase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutamate 5-kinase |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Molecular weight | Theoretical: 39.103457 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSDSQTLVVK LGTSVLTGGS RRLNRAHIVE LVRQCAQLHA AGHRIVIVTS GAIAAGREHL GYPELPATIA SKQLLAAVGQ SRLIQLWEQ LFSIYGIHVG QMLLTRADME DRERFLNARD TLRALLDNNI VPVINENDAV ATAEIKVGDN DNLSALAAIL A GADKLLLL ...String: MSDSQTLVVK LGTSVLTGGS RRLNRAHIVE LVRQCAQLHA AGHRIVIVTS GAIAAGREHL GYPELPATIA SKQLLAAVGQ SRLIQLWEQ LFSIYGIHVG QMLLTRADME DRERFLNARD TLRALLDNNI VPVINENDAV ATAEIKVGDN DNLSALAAIL A GADKLLLL TDQKGLYTAD PRSNPQAELI KDVYGIDDAL RAIAGDSVSG LGTGGMSTKL QAADVACRAG IDTIIAAGSK PG VIGDVME GISVGTLFHA QATPLENRKR WIFGAPPAGE ITVDEGATAA ILERGSSLLP KGIKSVTGNF SRGEVIRICN LEG RDIAHG VSRYNSDALR RIAGHHSQEI DAILGYEYGP VAVHRDDMIT R UniProtKB: Glutamate 5-kinase |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 865 / 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
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |