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Yorodumi- PDB-2ezc: AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI, NMR, 14 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ezc | ||||||
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Title | AMINO TERMINAL DOMAIN OF ENZYME I FROM ESCHERICHIA COLI, NMR, 14 STRUCTURES | ||||||
Components | PHOSPHOTRANSFERASE SYSTEM, ENZYME I | ||||||
Keywords | PHOSPHOTRANSFERASE / TRANSFERASE / KINASE / SUGAR TRANSPORT | ||||||
Function / homology | Function and homology information phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Clore, G.M. / Tjandra, N. / Garrett, D.S. / Gronenborn, A.M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Authors: Tjandra, N. / Garrett, D.S. / Gronenborn, A.M. / Bax, A. / Clore, G.M. #1: Journal: Biochemistry / Year: 1997 Title: Solution Structure of the 30 kDa N-Terminal Domain of Enzyme I of the Escherichia Coli Phosphoenolpyruvate:Sugar Phosphotransferase System by Multidimensional NMR Authors: Garrett, D.S. / Seok, Y.J. / Liao, D.I. / Peterkofsky, A. / Gronenborn, A.M. / 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 | 2ezc.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2ezc.ent.gz | 974 KB | Display | PDB format |
PDBx/mmJSON format | 2ezc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ezc_validation.pdf.gz | 341.5 KB | Display | wwPDB validaton report |
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Full document | 2ezc_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 2ezc_validation.xml.gz | 68.4 KB | Display | |
Data in CIF | 2ezc_validation.cif.gz | 90 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/2ezc ftp://data.pdbj.org/pub/pdb/validation_reports/ez/2ezc | 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: 28381.316 Da / Num. of mol.: 1 / Fragment: AMINO-TERMINAL DOMAIN RESIDUES 1 - 259 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GI698 / Plasmid: PLP2 / Production host: Escherichia coli (E. coli) References: UniProt: P08839, phosphoenolpyruvate-protein phosphotransferase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE 3D STRUCTURE OF THE EIN WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 4369 EXPERIMENTAL NMR RESTRAINTS: 117 T1/T2 RESTRAINTS; 952 SEQUENTIAL (|I- J|=1), 809 MEDIUM RANGE ...Text: THE 3D STRUCTURE OF THE EIN WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR NMR AND IS BASED ON 4369 EXPERIMENTAL NMR RESTRAINTS: 117 T1/T2 RESTRAINTS; 952 SEQUENTIAL (|I- J|=1), 809 MEDIUM RANGE (1 < |I-J| <=5) AND 586 LONG RANGE (|I-J| >5) INTERRESIDUES AND 471 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 230 DISTANCES FOR 115 BACKBONE HYDROGEN BONDS; 543 TORSION ANGLE RESTRAINTS; 163 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 498 (257 CALPHA AND 241 CBETA) 13C SHIFT. RESTRAINTS. (NUMBERS OF RESIDUES 1 - 259) |
-Sample preparation
Sample conditions | pH: 7.5 / Temperature: 313 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: simulated annealing / Software ordinal: 1 Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103) AND CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, AND T1/T2 RESTRAINTS (TJANDRA ET AL. NATURE STRUCT. BIOL. 4, 443-449, 1997). IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. BEST FITTING TO GENERATE THE AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 1 - 246 (RESIDUES 250 - 259 ARE DISORDERED IN SOLUTION). THE DIFFUSION AXIS IS REPRESENTED BY A LINE CONNECTING THE FOLLOWING POINTS: MODEL 1 P1 98.704 -8.634 6.291 P2 100.199 -8.778 6.547 MODEL 2 P1 98.931 -5.748 10.946 P2 100.415 -5.983 11.191 MODEL 3 P1 99.599 -3.491 4.832 P2 101.089 -3.639 5.107 MODEL 4 P1 98.518 -10.247 4.022 P2 100.021 -10.426 4.194 MODEL 5 P1 98.892 -9.643 8.429 P2 100.382 -9.849 8.666 MODEL 6 P1 98.187 -10.433 9.895 P2 99.687 -10.622 10.090 MODEL 7 P1 98.045 -10.499 13.089 P2 99.524 -10.671 13.411 MODEL 8 P1 99.528 -4.087 7.695 P2 101.004 -4.267 8.022 MODEL 9 P1 98.685 -8.524 9.303 P2 100.183 -8.747 9.462 MODEL 10 P1 99.072 -8.432 7.916 P2 100.564 -8.633 8.149 MODEL 11 P1 99.021 -6.823 7.559 P2 100.509 -6.952 7.857 MODEL 12 P1 98.326 -9.444 11.667 P2 99.823 -9.615 11.894 MODEL 13 P1 98.562 -11.334 4.771 P2 100.052 -11.528 5.020 MODEL 14 P1 99.482 -4.480 4.665 P2 100.959 -4.700 4.955 | ||||||||||||
NMR ensemble | Conformers calculated total number: 30 / Conformers submitted total number: 14 |