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Yorodumi- PDB-1afj: STRUCTURE OF THE MERCURY-BOUND FORM OF MERP, THE PERIPLASMIC PROT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1afj | ||||||
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Title | STRUCTURE OF THE MERCURY-BOUND FORM OF MERP, THE PERIPLASMIC PROTEIN FROM THE BACTERIAL MERCURY DETOXIFICATION SYSTEM, NMR, 20 STRUCTURES | ||||||
Components | MERP | ||||||
Keywords | MERCURY DETOXIFICATION / PERIPLASMIC / HEAVY METAL TRANSPORT / ALPHA-BETA SANDWICH | ||||||
Function / homology | Function and homology information mercury ion transmembrane transporter activity / mercury ion binding / periplasmic space Similarity search - Function | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | SOLUTION NMR / DISTANCE GEOMETRY SIMULATED ANNEALING | ||||||
Authors | Steele, R.A. / Opella, S.J. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Structures of the reduced and mercury-bound forms of MerP, the periplasmic protein from the bacterial mercury detoxification system. Authors: Steele, R.A. / Opella, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1afj.cif.gz | 417.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1afj.ent.gz | 346.9 KB | Display | PDB format |
PDBx/mmJSON format | 1afj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1afj_validation.pdf.gz | 337 KB | Display | wwPDB validaton report |
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Full document | 1afj_full_validation.pdf.gz | 532.2 KB | Display | |
Data in XML | 1afj_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 1afj_validation.cif.gz | 76.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/1afj ftp://data.pdbj.org/pub/pdb/validation_reports/af/1afj | 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: 7483.630 Da / Num. of mol.: 1 / Fragment: ENTIRE PROTEIN Source method: isolated from a genetically manipulated source Details: THE PROTEIN STUDIED EXCLUDES THE PRECURSOR SIGNAL SEQUENCE. THIS IS THE NATIVE FORM OF THE PROTEIN AFTER CELL PROCESSING. Source: (gene. exp.) Shigella flexneri (bacteria) / Description: MER GENES LOCATED ON TRANSPOSON TN21 / Cellular location: PERIPLASM / Gene: MERP / Plasmid: PSSS / Species (production host): Escherichia coli / Gene (production host): MERP / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04129 |
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#2: Chemical | ChemComp-HG / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 6.5 / Temperature: 300 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Method: DISTANCE GEOMETRY SIMULATED ANNEALING / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. IN SUMMARY, INITIAL CALCULATIONS WERE STARTED FROM A LINEAR POLYPEPTIDE TEMPLATE WITH RANDOM BACKBONE ANGLES. AN ITERATIVE ...Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. IN SUMMARY, INITIAL CALCULATIONS WERE STARTED FROM A LINEAR POLYPEPTIDE TEMPLATE WITH RANDOM BACKBONE ANGLES. AN ITERATIVE REFINEMENT WAS EMPLOYED USING ADDITIONAL RESTRAINTS AS THE QUALITY OF THE STRUCTURES IMPROVED AND AMBIGUITIES IN THE DATA WERE RESOLVED. | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 80 / Conformers submitted total number: 20 |