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Yorodumi- PDB-1wcr: Trimeric Structure of the Enzyme IIA from Escherichia coli Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wcr | ||||||
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Title | Trimeric Structure of the Enzyme IIA from Escherichia coli Phosphotransferase System Specific for N,N'-Diacetylchitobiose | ||||||
Components | PTS SYSTEM, N, N'-DIACETYLCHITOBIOSE-SPECIFIC IIA COMPONENT | ||||||
Keywords | TRANSFERASE / IIA / PTS / MUTAGENESIS / CHITOBIOSE / SUGAR TRANSPORT / PHOSPHOTRANSFERASE | ||||||
Function / homology | Function and homology information protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING IN TORSION ANG SPACE | ||||||
Model type details | MINIMIZED AVERAGE | ||||||
Authors | Tang, C. / Clore, G.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Solution Structure of Enzyme Iiachitobiose from the N,N'-Diacetylchitobiose Branch of the Escherichia Coli Phosphotransferase System Authors: Tang, C. / Williams, D.C. / Ghirlando, R. / Clore, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wcr.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wcr.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 1wcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wcr_validation.pdf.gz | 344.6 KB | Display | wwPDB validaton report |
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Full document | 1wcr_full_validation.pdf.gz | 354.4 KB | Display | |
Data in XML | 1wcr_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1wcr_validation.cif.gz | 10.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/1wcr ftp://data.pdbj.org/pub/pdb/validation_reports/wc/1wcr | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11256.186 Da / Num. of mol.: 3 / Fragment: RESIDUES 14-116 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P17335, UniProt: P69791*PLUS, protein-Npi-phosphohistidine-sugar phosphotransferase Compound details | ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: EXPERIMENTAL RESTRAINTS: 1290 INTERPROTON DISTANCE RESTRAINTS: 246 SEQUENTIAL, 258 MEDIUM-RANGE, 90 LONG-RANGE INTRAMOLECULAR RESTRAINTS; 234 INTERMOLECULAR DISTANCE RESTRAINTS; 462 DISTANCE ...Text: EXPERIMENTAL RESTRAINTS: 1290 INTERPROTON DISTANCE RESTRAINTS: 246 SEQUENTIAL, 258 MEDIUM-RANGE, 90 LONG-RANGE INTRAMOLECULAR RESTRAINTS; 234 INTERMOLECULAR DISTANCE RESTRAINTS; 462 DISTANCE RESTRAINTS FOR BACKBONE H-BONDS FOR 231 H-BONDS (71 PER SUBUNIT) 729 TORSION ANGLE RESTRAINTS (255 PHI, 255 PSI, 219 CHI) 585 CALPHA/CBETA CHEMICAL SHIFT RESTRAINTS 759 RESIDUAL DIPOLAR COUPLING RESTRAINTS (252 N-H, 255 N-C', 249 C'-CA) DIPOLAR COUPLING R-FACTORS FOR THE RESTRAINED REGULARIZED MEAN STRUCTURE N-H 7.1% N-C' 15.2% C'-CA 17.7% |
-Sample preparation
Sample conditions | Ionic strength: 10MM SODIUM PHOSPHATE / pH: 6.5 / Pressure: 1.0 atm / Temperature: 303.0 K |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: SIMULATED ANNEALING IN TORSION ANG SPACE / Software ordinal: 1 Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, 13CALPHA/BETA CHEMICAL SHIFT RESTRAINTS, AND RESIDUAL DIPOLAR COUPLING ...Details: THE TARGET FUNCTION COMPRISES TERMS FOR THE NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, 13CALPHA/BETA CHEMICAL SHIFT RESTRAINTS, AND RESIDUAL DIPOLAR COUPLING RESTRAINTS (N-H, N-C' AND C'-CA). NON-BONDED INTERACTIONS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, TORSION ANGLE AND HYDROGEN BONDING DATABASE POTENTIALS OF MEAN FORCE, AND A RADIUS OF GYRATION RESTRAINT. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE ATOMIC RMS DIFFERENCE IN ANGSTROMS BETWEEN THE 80 INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATES RESIDUES 1-3, 61-69 AND 102-103 ARE DISORDERED IN SOLUTION. | ||||||||||||
NMR ensemble | Conformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE Conformers calculated total number: 100 / Conformers submitted total number: 1 |