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Yorodumi- PDB-3din: Crystal structure of the protein-translocation complex formed by ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3din | ||||||
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Title | Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / PROTEIN TRANSPORT / protein translocation / ATPase / ATP-binding / Inner membrane / Nucleotide-binding / Transport / Transmembrane | ||||||
Function / homology | Function and homology information protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein import / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / plasma membrane => GO:0005886 ...protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / protein import / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / plasma membrane => GO:0005886 / protein transmembrane transporter activity / protein secretion / protein targeting / membrane => GO:0016020 / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima MSB8 (bacteria) Thermotoga sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 4.5 Å | ||||||
Authors | Zimmer, J. / Nam, Y. / Rapoport, T.A. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Structure of a complex of the ATPase SecA and the protein-translocation channel. Authors: Zimmer, J. / Nam, Y. / Rapoport, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3din.cif.gz | 490.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3din.ent.gz | 398.4 KB | Display | PDB format |
PDBx/mmJSON format | 3din.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/3din ftp://data.pdbj.org/pub/pdb/validation_reports/di/3din | HTTPS FTP |
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-Related structure data
Related structure data | 3dl8C 1tf2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 100643.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: secA, TM_1578 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1R4 |
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-Preprotein translocase subunit ... , 3 types, 6 molecules CFDGEH
#2: Protein | Mass: 48217.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: secY, TM_1480 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1I9 #3: Protein | Mass: 7322.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: secE, TM_0452 / Production host: Escherichia coli (E. coli) / References: UniProt: P35874 #4: Protein | Mass: 8251.904 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga sp. (bacteria) / Strain: RQ2 / Gene: secG, TRQ2_0456 / Production host: Escherichia coli (E. coli) / References: UniProt: B1L914, UniProt: A0A0F6AK20*PLUS |
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-Non-polymers , 3 types, 6 molecules
#5: Chemical | #6: Chemical | #7: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.32 Å3/Da / Density % sol: 71.5 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 20% PEG 3350, 200mM (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 4.5→50 Å / Num. obs: 34733 / % possible obs: 97.7 % / Redundancy: 11.6 % / Rsym value: 0.065 / Net I/σ(I): 16.1 | ||||||||||||||||||||||||
Reflection shell | Resolution: 4.5→4.77 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2 / Rsym value: 0.85 / % possible all: 89.7 |
-Phasing
Phasing |
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-Processing
Software |
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Refinement | Method to determine structure: SAD, MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TF2 Resolution: 4.5→15 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 358.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4.5→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.5→4.77 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |