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- PDB-2v93: EQUILLIBRIUM MIXTURE OF OPEN AND PARTIALLY-CLOSED SPECIES IN THE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2v93 | ||||||
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Title | EQUILLIBRIUM MIXTURE OF OPEN AND PARTIALLY-CLOSED SPECIES IN THE APO STATE OF MALTODEXTRIN-BINDING PROTEIN BY PARAMAGNETIC RELAXATION ENHANCEMENT NMR | ||||||
![]() | MALTOSE-BINDING PERIPLASMIC PROTEIN | ||||||
![]() | TRANSPORT PROTEIN / MBP / PRE / PERIPLASM / TRANSPORT / DOMAIN MOTION / RAPID CONFORMATIONAL EXCHANGE / SUGAR TRANSPORT / MINOR SPECIES IN SOLUTION | ||||||
Function / homology | ![]() detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE SIMULATED ANNEALING DYNAMICS | ||||||
![]() | Clore, G.M. / Tang, C. | ||||||
![]() | ![]() Title: Open-to-Closed Transition in Apo Maltose-Binding Protein Observed by Paramagnetic NMR. Authors: Tang, C. / Schwieters, C.D. / Clore, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3.9 MB | Display | ![]() |
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PDB format | ![]() | 3.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 460.2 KB | Display | |
Data in CIF | ![]() | 724.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: Protein | Mass: 40757.273 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | Compound details | ENGINEERED | Nonpolymer details | 4-MALEIMIDE-TEMPO, 4-MALEIMIDE-2,2,6, 6-TETRAMETHYL-PIPERIDINE-1-OXYL (MXT): COVALENTLY CONJUGATED ...4-MALEIMIDE-TEMPO, 4-MALEIMIDE-2,2,6, 6-TETRAMETHY | Sequence details | MUTATIONS OF D41C AND S211C, ONE AT A TIME | |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: REFINEMENT OF THE MINOR FORM OF APO MBP WAS CARRIED OUT BY CONJOINED RIGID BODY AND TORSION ANGLE SIMULATED ANNEALING SUBJECT TO A TARGET FUNCTION COMPRISING A PRE PEUDOPOTENTIAL, A QUARTIC VAN ...Text: REFINEMENT OF THE MINOR FORM OF APO MBP WAS CARRIED OUT BY CONJOINED RIGID BODY AND TORSION ANGLE SIMULATED ANNEALING SUBJECT TO A TARGET FUNCTION COMPRISING A PRE PEUDOPOTENTIAL, A QUARTIC VAN DER WAALS REPULSION TERM TO PREVENT ATOMIC OVERLAP, A MULTIDIMENSIONAL TORSION ANGLE DATABASE OF MEAN FORCE, AND APPROPRIATE TORSION ANGLE AND HYDROGEN BONDING DISTANCE RESTRAINTS WITHIN THE LINKER. THE CALCULATED GAMMA2 RATES ARE GIVEN BY A POPULATION WEIGHTED AVERAGE OF THE GAMMA2 RATES OF THE MAJOR (OPEN, 1OMP) AND MINOR STATES OF MBP. THE MINOR FORM OF APO MBP ( 5 PERCENT OCCUPANCY, CHAIN C) IS REPRESENTED BY A SECOND CONFORMER ALLOWING RIGID-BODY INTERDOMAIN MOVEMENT BY GIVING THE LINKER REGIONS (RESIDUES 106-114, 252-265 AND 314-333) FULL TORSIONAL DEGREES OF FREEDOM (WITH THE EXCEPTION OF THE HELIX, RESIDUES 315-326, WHOSE BACKBONE IS ALSO TREATED AS A RIGID BODY). THE STRUCTURE OF THE MAJOR (95 PERCENT OCCUPANCY, CHAIN O) IS FIXED DURING THE CALCULATION TO THAT OF THE CRYSTAL STRUCTURE OF APO MBP ( 1OMP). THE PARAMAGNETIC PROBES (MALEIMIDE-TEMPO, MXT) AT POSITIONS 41 (D41C) AND 211 (S211C) ARE REPRESENTED BY A SIX-CONFORMER ENSEMBLE FOR BOTH THE MAJOR OPEN AND MINOR CLOSED STATES (ALTLOC A-F, A-C AND D-F ARE FOR THE TWO DIFFERENT ENANTIOMERS OF CONJUGATED MALEIMIDE-TEMPO). ONLY THE BACKBONE COORDINATES AND THE COORDINATES OF THE PARAMAGNETIC PROBE (RESIDUES 500 AND 600) ARE DEPOSITED. |
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Sample preparation
Details | Contents: 10MM TRIS-HCL |
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Sample conditions | Ionic strength: 0MM NACL / pH: 7.4 / Pressure: 1.0 atm / Temperature: 310.0 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: CONJOINED RIGID BODY, TORSION ANGLE SIMULATED ANNEALING DYNAMICS Software ordinal: 1 | |||||||||
NMR ensemble | Conformer selection criteria: PRE AND VDW ENERGIES / Conformers calculated total number: 100 / Conformers submitted total number: 50 |