+Open data
-Basic information
Entry | Database: PDB / ID: 8zpj | ||||||
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Title | EcGK bundle at APO state. | ||||||
Components | Glutamate 5-kinase | ||||||
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 / magnesium ion binding / protein homodimerization activity / RNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.97 Å | ||||||
Authors | Zhang, T. / Leng, Q. / Liu, L.J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: EcGPR tetramer with catalytic intermediates Authors: Zhang, T. / Leng, Q. / Liu, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zpj.cif.gz | 636.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zpj.ent.gz | 428.2 KB | Display | PDB format |
PDBx/mmJSON format | 8zpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zpj_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8zpj_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8zpj_validation.xml.gz | 86.6 KB | Display | |
Data in CIF | 8zpj_validation.cif.gz | 128.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/8zpj ftp://data.pdbj.org/pub/pdb/validation_reports/zp/8zpj | HTTPS FTP |
-Related structure data
Related structure data | 60346MC 8zriC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 39103.457 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: proB, b0242, JW0232 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P0A7B5, glutamate 5-kinase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: EcGK at APO state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: Rosetta |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||
Helical symmerty | Angular rotation/subunit: 85.85 ° / Axial rise/subunit: 21 Å / Axial symmetry: C1 | ||||||||||||||||
3D reconstruction | Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 512330 / Symmetry type: HELICAL | ||||||||||||||||
Refinement | Cross valid method: NONE |