- PDB-1m23: STRUCTURE OF THE DIMERIZED CYTOPLASMIC DOMAIN OF P23 IN SOLUTION -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1m23
Title
STRUCTURE OF THE DIMERIZED CYTOPLASMIC DOMAIN OF P23 IN SOLUTION
Components
PROTEIN (P23)
Keywords
MEMBRANE PROTEIN / TRANSPORT / PROTEIN TRANSPORT / TRANSMEMBRANE / GLYCOPROTEIN / VESICULAR TRANSPORT / COP / COATOMER / GOLGI STACK / SOLUTION STRUCTURE / P23 FAMILY
Function / homology
Function and homology information
COPI-coated vesicle budding / protein localization to ERGIC / cytosol to ERGIC protein transport / regulation of amyloid-beta formation / COPI-coated vesicle / gamma-secretase complex / zymogen granule membrane / regulated exocytosis / positive regulation of interleukin-1 production / trans-Golgi network transport vesicle ...COPI-coated vesicle budding / protein localization to ERGIC / cytosol to ERGIC protein transport / regulation of amyloid-beta formation / COPI-coated vesicle / gamma-secretase complex / zymogen granule membrane / regulated exocytosis / positive regulation of interleukin-1 production / trans-Golgi network transport vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / transport vesicle membrane / COPII-coated ER to Golgi transport vesicle / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / protein transmembrane transporter activity / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / secretory granule membrane / positive regulation of protein secretion / intracellular protein transport / melanosome / Golgi membrane / endoplasmic reticulum membrane / plasma membrane Similarity search - Function
Mass: 1717.129 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN / Source method: obtained synthetically Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED FROM THE GOLGI STACK OF THE ER (ENDOPLASMIC RETICULUM) OF NEW ZEALAND WHITE RABBIT (ORYCTOLAGUS CUNICULUS) LIVER CELLS. References: UniProt: Q28735
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
NOESY
1
2
1
COSY
1
3
1
CLEAN-TOCSY
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Sample preparation
Sample conditions
Ionic strength: 650 mM / pH: 3.6 / Pressure: 10E+5 PA atm / Temperature: 280 K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
NMR spectrometer
Type: Bruker DRX 600 / Manufacturer: Bruker / Model: DRX 600 / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
X-PLOR
3.84
BRUNGER, NILGES
refinement
NDEE
2
structuresolution
X-PLOR
3.84
structuresolution
Refinement
Method: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 Details: STRATEGY USED FOR NMR STRUCTURE CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS-PEAKS WERE INCORPORATED INTO THE STRUCTURE ...Details: STRATEGY USED FOR NMR STRUCTURE CALCULATION: EXPERIMENTAL RESTRAINTS FOR THE STRUCTURE CALCULATIONS INITIALLY, FREQUENCY DEGENERATED NOESY CROSS-PEAKS WERE INCORPORATED INTO THE STRUCTURE CALCULATION AS 'AMBIGUOUS'. SUBSEQUENTLY, THE PROTON-PROTON DISTANCES IN THE CALCULATED STRUCTURES WERE DETERMINED USING THE PROGRAM 'BACKCALC_DB 2.0' (SOFTWARE SYMBIOSE, INC., BAYREUTH, GERMANY) AND COMPARED WITH THE COMBINATIONS OF DISTANCES POSSIBLE FOR EACH FREQUENCY DEGENERATED NOESY CROSS-PEAK. IF ONLY ONE OF THE POSSIBLE DISTANCE COMBINATIONS WAS FULFILLED IN MORE THAN 50% OF THE CALCULATED STRUCTURES, THE DISTANCE INFORMATION WAS USED IN FURTHER STRUCTURE CALCULATIONS. THIS PROCEDURE WAS REPEATED SEVERAL TIMES, LEADING TO A TOTAL OF 223 INTRARESIDUAL AND 249 INTERRESIDUAL NOE CONNECTIVITIES. STRUCTURE CALCULATIONS STRUCTURES CALCULATIONS WERE PERFORMED USING A MODIFIED AB INITIO SIMULATED ANNEALING PROTOCOL (NILGES, UNPUBLISHED) WITH X-PLOR V3.840. THE CALCULATION STRATEGY INCLUDES FLOATING ASSIGNMENT OF PROCHIRAL GROUPS AND A REDUCED PRESENTATION FOR NON-BONDED INTERACTIONS FOR PART OF THE CALCULATION TO INCREASE EFFICIENCY. A MORE DETAILED DESCRIPTION OF THE PROTOCOL IS GIVEN IN KHARRAT ET AL. (EMBO J. 14 (1995) 3572-84). STRUCTURE PARAMETERS WERE EXTRACTED FROM THE STANDARD FILES PARALLHDG.PRO AND TOPALLHDG.PRO OF X-PLOR V3.840. IN EACH ROUND OF THE STRUCTURE CALCULATION 100 STRUCTURES WERE CALCULATED. OF THE 100 STRUCTURES RESULTING FROM THE FINAL ROUND OF STRUCTURE CALCULATION, THOSE 30 STRUCTURES THAT SHOWED THE LOWEST TOTAL ENERGY VALUES WERE SELECTED FOR FURTHER CHARACTERIZATION.
NMR ensemble
Conformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA Conformers calculated total number: 30 / Conformers submitted total number: 10
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