- PDB-2mlh: NMR Solution Structure of Opa60 from N. Gonorrhoeae in FC-12 Micelles -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2mlh
Title
NMR Solution Structure of Opa60 from N. Gonorrhoeae in FC-12 Micelles
Components
Opacity protein opA60
Keywords
MEMBRANE PROTEIN / BETA-BARREL
Function / homology
Porin, opacity type / Opacity family porin protein / Outer membrane autotransporter barrel / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / porin activity / Cell surface interactions at the vascular wall / cell outer membrane / Opacity protein opA60
Mass: 27115.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: MS11 / Gene: opaH / Production host: neisseria gonorrhoeae (bacteria) / References: UniProt: Q04884
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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
2D 1H-15N HSQC
1
2
1
3DHN(COCA)CB
1
3
1
3D HN(CA)CB
1
4
1
3D HNCO
1
5
1
3D HNCA
1
6
1
3D 1H-15N NOESY
1
7
1
3DHN(CO)CA
1
8
1
3DHN(CA)CO
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Sample preparation
Details
Contents: 800 uM [U-100% 13C; U-100% 15N; U-80% 2H] OPA60, 150 mM Dodecyl Phosphcholine, 20 mM sodium phosphate, 150 mM sodium chloride, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Isotopic labeling
Solution-ID
800uM
OPA60-1
[U-100% 13C; U-100% 15N; U-80% 2H]
1
150mM
Dodecyl Phosphcholine-2
1
20mM
sodium phosphate-3
1
150mM
sodium chloride-4
1
Sample conditions
pH: 6.2 / Pressure: ambient / Temperature: 313 K
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
600
1
Bruker Avance
Bruker
AVANCE
800
2
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Processing
NMR software
Name
Version
Developer
Classification
X-PLOR NIH
2.31
Schwieters, Kuszewski, TjandraandClore
structuresolution
CARA
1.8.4.2
KellerandWuthrich
chemicalshiftassignment
NMRPipe
7.9
Delaglio, Grzesiek, Vuister, Zhu, PfeiferandBax
dataanalysis
TopSpin
3
BrukerBiospin
collection
X-PLOR NIH
Schwieters, Kuszewski, TjandraandClore
refinement
Refinement
Method: simulated annealing / Software ordinal: 1
NMR constraints
Protein phi angle constraints total count: 64 / Protein psi angle constraints total count: 64
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 400 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 1.5 Å / Maximum upper distance constraint violation: 6.5 Å
NMR ensemble rms
Distance rms dev: 0.11 Å / Distance rms dev error: 0.002 Å
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