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Yorodumi- PDB-2mly: NMR structure of E. coli Trigger Factor in complex with unfolded ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2mly | ||||||
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Title | NMR structure of E. coli Trigger Factor in complex with unfolded PhoA1-150 | ||||||
Components |
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Keywords | CHAPERONE / molecular chaperone / unfolded protein | ||||||
Function / homology | Function and homology information Trigger factor, domain 2 / Trigger factor, C-terminal domain / Trigger factor ribosome-binding domain / Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Saio, T. / Guan, X. / Rossi, P. / Economou, A. / Kalodimos, C.G. | ||||||
Citation | Journal: Science / Year: 2014 Title: Structural basis for protein antiaggregation activity of the trigger factor chaperone. Authors: Saio, T. / Guan, X. / Rossi, P. / Economou, A. / Kalodimos, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mly.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2mly.ent.gz | 1.4 MB | Display | PDB format |
PDBx/mmJSON format | 2mly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mly_validation.pdf.gz | 444.5 KB | Display | wwPDB validaton report |
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Full document | 2mly_full_validation.pdf.gz | 555.1 KB | Display | |
Data in XML | 2mly_validation.xml.gz | 109 KB | Display | |
Data in CIF | 2mly_validation.cif.gz | 166.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/2mly ftp://data.pdbj.org/pub/pdb/validation_reports/ml/2mly | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 49696.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tig, BN896_0318 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U6N325, peptidylprolyl isomerase |
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#2: Protein | Mass: 15905.933 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phoA, BN896_0267 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U6N3P1 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-100% 13C; U-100% 15N] Alkaline phosphatase, 0.5 mM [U-100% 13C; U-100% 15N] Trigger Factor, 100 mM potassium chloride, 3 mM BME, 20 mM potassium phosphate, 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 7 / Pressure: ambient / Temperature: 295 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1896 / NOE intraresidue total count: 375 / NOE long range total count: 781 / NOE medium range total count: 257 / NOE sequential total count: 483 | ||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 1000 / Conformers submitted total number: 10 | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.04 Å |