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Yorodumi- PDB-2wwv: NMR structure of the IIAchitobiose-IIBchitobiose complex of the N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wwv | ||||||
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Title | NMR structure of the IIAchitobiose-IIBchitobiose complex of the N,N'- diacetylchitoboise brance of the E. coli phosphotransferase system. | ||||||
Components |
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Keywords | TRANSFERASE / KINASE / PHOSPHOTRANSFERASE SYSTEM / CHITOBIOSE / SUGAR TRANSPORT | ||||||
Function / homology | Function and homology information protein-Npi-phosphohistidine-N,N'-diacetylchitobiose phosphotransferase / protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) ESCHERICHIA COLI K-12 (bacteria) | ||||||
Method | SOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE SIMULATED ANNEALING | ||||||
Model type details | MINIMIZED AVERAGE, MODEL 1 | ||||||
Authors | Sang, Y.S. / Cai, M. / Clore, G.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Solution Structure of the Iiachitobose-Iibchitobiose Complex of the N,N'-Diacetylchitobiose Branch of the Escherichia Coli Phosphotransfer System Authors: Jung, Y.S. / Cai, M. / Clore, G.M. #1: Journal: J.Biol.Chem. / Year: 2005 Title: Solution Structure of Enzyme Iia(Chitobiose) from the N,N'-Diacetylchitobiose Branch of the Escherichia Coli Phosphotransferase System. Authors: Tang, C. / Williams, D.C.J. / Ghirlando, R. / Clore, G.M. #2: Journal: Structure / Year: 1997 Title: The Structure of an Energy-Coupling Protein from Bacteria, Iibcellobiose, Reveals Similarity to Eukaryotic Protein Tyrosine Phosphatases. Authors: Van Montfort, R.L. / Pijning, T. / Kalk, K.H. / Reizer, J. / Saier, M.H.J. / Thunnissen, M.M. / Robillard, G.T. / Dijkstra, B.W. #3: Journal: J.Mol.Biol. / Year: 2001 Title: NMR Structure of Cysteinyl-Phosphorylated Enzyme Iib of the N,N'-Diacetylchitobiose-Specific Phosphoenolpyruvate-Dependent Phosphotransferase System of Escherichia Coli. Authors: Ab, E. / Schuurman-Wolters, G.K. / Nijlant, D. / Dijkstra, K. / Saier, M.H. / Robillard, G.T. / Scheek, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wwv.cif.gz | 10.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwv.ent.gz | 9.3 MB | Display | PDB format |
PDBx/mmJSON format | 2wwv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wwv_validation.pdf.gz | 370.8 KB | Display | wwPDB validaton report |
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Full document | 2wwv_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2wwv_validation.xml.gz | 621.3 KB | Display | |
Data in CIF | 2wwv_validation.cif.gz | 875.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwv ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwv | 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: 11247.152 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) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) References: UniProt: P69791, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Protein | | Mass: 11049.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) References: UniProt: P69795, protein-Npi-phosphohistidine-sugar phosphotransferase Compound details | ENGINEERED RESIDUE IN CHAIN A, HIS 89 TO GLU ENGINEERED RESIDUE IN CHAIN A, ASP 92 TO LEU ...ENGINEERED | Sequence details | RESIDUE 1 IN CHAINS A, B AND C CORRESPONDS TO RESIDUE 14 OF WILD TYPE IIACHB, RESIDUE 76 IS A HIS ...RESIDUE 1 IN CHAINS A, B AND C CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: NONE |
-Sample preparation
Sample conditions | pH: 6.5 / Temperature: 308.0 K |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: CONJOINED RIGID BODY, TORSION ANGLE SIMULATED ANNEALING Software ordinal: 1 Details: THE STRUCTURE OF THE COMPLEX WAS SOLVED BY CONJOINED RIGID BODY/TORSION ANGLE SIMULATED ANNEALING USING XPLOR-NIH. THE CALCULATIONS ARE BASED ON 40 INTERMOLECULAR INTERPROTON DISTANCE ...Details: THE STRUCTURE OF THE COMPLEX WAS SOLVED BY CONJOINED RIGID BODY/TORSION ANGLE SIMULATED ANNEALING USING XPLOR-NIH. THE CALCULATIONS ARE BASED ON 40 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS, 78 INTRAMOLECULAR INTERPROTON DISTANCE RESTRAINTS RELATED ONLY TO THE ACTIVE SITE LOOP OF IIBCHB, 82 TORSION ANGLE RESTRAINTS RELATED TO THE BACKBONE OF THE ACTIVE SITE LOOP OF IIBCHB (RESIDUES 9-16, CHAIN D) AND THE INTERFACIAL SIDE CHAINS, 153 DIPOLAR COUPLINGS RELATED TO IIBCHB, AND 15 13CALPHA/13CBETA CHEMICAL SHIFT RESTRAINTS RELATED TO THE ACTIVE SITE LOOP OF IIBCHB. WITH THE EXCEPTION OF THE ACTIVE SITE LOOP OF IIBCHB (RESIDUES 9-16 OF CHAIN D) AND A MOBILE LOOP OF IIACHB (RESIDUES 62-71 OF CHAINS A, B, C) THE BACKBONE OF THE TWO PROTEINS AND NON-INTERFACIAL SIDE CHAINS ARE TREATED AS RIGID BODIES WITH ROTATIONAL AND TRANSLATIONAL DEGREES OF FREEDOM. THE COORDINATES FOR THE PORTIONS TREATED AS RIGID BODIES ARE TAKEN FROM THE X-RAY STRUCTURE OF IIBCHB (PDB CODE 1IIB) AND THE NMR STRUCTURE OF IIACHB (PDB CODE 1WCR). THE BACKBONE OF RESIDUES 9-16 OF CHAIN D, 62-71 OF CHAINS A, B AND C, AND THE INTERFACIAL SIDE CHAINS ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM. THE TARGET FUNCTION COMPRISES NOE-DERIVED INTERPROTON DISTANCE RESTRAINTS, TORSION ANGLE RESTRAINTS, RDC RESTRAINTS, 13CALPHA/13CBETA CHEMICAL SHIFT RESTRAINTS, A QUARTIC VAN DER WAALS REPULSION TERM FOR THE NON-BONDED CONTACTS, A MULTIDIMENSIONAL TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE, AND A GYRATION VOLUME POTENTIAL TO ENSURE OPTIMAL PACKING. FURTHER DETAILS ARE GIVEN IN THE ASSOCIATED PUBLICATION. | ||||||||||||
NMR ensemble | Conformer selection criteria: RESTRAINED REGULARIZED MEAN / Conformers calculated total number: 91 / Conformers submitted total number: 91 |