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Open data
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Basic information
Entry | Database: PDB / ID: 2lrv | ||||||
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Title | Assignment of E coli periplasmic protein YmgD | ||||||
![]() | Uncharacterized protein ymgD | ||||||
![]() | UNKNOWN FUNCTION | ||||||
Function / homology | YmgD protein / Uncharacterised protein YmgD / YmgD domain superfamily / YmgD protein / 10k-s Protein, Hypothetical Protein A; Chain A / outer membrane-bounded periplasmic space / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YmgD![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Wu, K. / Inouye, M. / Baum, J. / Hsu, S. / Masuda, H. | ||||||
![]() | ![]() Title: Solution structure of homodimeric periplasmic protein YmgD in E. coli Authors: Wu, K. / Masuda, H. / Hsu, S.D. / Baum, J. / Inouye, 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 | ![]() | 485.1 KB | Display | ![]() |
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PDB format | ![]() | 409.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 541.1 KB | Display | ![]() |
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Full document | ![]() | 745.3 KB | Display | |
Data in XML | ![]() | 48.6 KB | Display | |
Data in CIF | ![]() | 59.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 9737.120 Da / Num. of mol.: 1 / Fragment: UNP residues 20-109 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Contents: 0.4 mM [U-99% 13C; U-99% 15N] YmgD, 90 % H2O, 10 % D2O, 100 mM Sodium acetate, 50 mM NaCl, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.05 / pH: 5 / Pressure: ambient / Temperature: 308 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: NOE, Dihedral angles, RDC and symmetry restraints, explicit solvent refinement and full electrostatics | ||||||||||||
NMR constraints | NOE constraints total: 1045 / NOE intraresidue total count: 260 / NOE long range total count: 94 / NOE medium range total count: 315 / NOE sequential total count: 376 | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.2 Å / Maximum upper distance constraint violation: 0.5 Å |