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139555
Biological Macromolecular Structures Enabling Breakthroughs in Research and Education
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Structure Summary
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Sequence
Sequence Similarity
Structure Similarity
Experiment
1GHH
SOLUTION STRUCTURE OF DINI
Display Files
FASTA Sequence
PDB File
PDB File (Header)
mmCIF File
mmCIF File (Header)
PDBML/XML File
PDBML/XML File (Header)
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FASTA Sequence
PDB File (Text)
PDB File (gz)
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PDBx/mmCIF File (gz)
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PDBML/XML File (gz)
NMR Restraints (Text)
NMR Restraints (gz)
V2 NMR Restraints (gz)
SOLUTION NMR Experimental Data
Experimental Details
Sample Conditions
Sample Contents
0.6 mM DinI U-13C,15N, 20 mM phosphate buffer, 100 mM NaCl; pH 6.6; 95% H2O, 5% D2O
Solvent
n/a
Ionic Strength
n/a
pH
6.6
Pressure
AMBIENT
Temperature (K)
298.0
Experiment(s):
3D_15N-separated_NOESY, 3D_13C-separated_NOESY, HNCG, HN(CO)CG
Sample Contents
0.6 mM DinI U-13C,15N, 20 mM phosphate buffer, 100 mM NaCl; pH 6.6; 99% D2O, 1% H2O
Solvent
n/a
Ionic Strength
n/a
pH
6.6
Pressure
AMBIENT
Temperature (K)
298.0
Experiment(s):
2D NOESY
Sample Contents
0.6 mM DinI U-13C,15N, 20 mM phosphate buffer, 100 mM NaCl; pH 6.6; BICELLE OR PHAGE LIQUID CRYSTAL, 95% H2O, 5% D2O
Solvent
n/a
Ionic Strength
n/a
pH
6.6
Pressure
AMBIENT
Temperature (K)
298.0
Experiment(s):
IPAP_15N_HSQC, HNCO, (HA)CA(CO)NH
Spectrometer Information
Manufacturer
Model
Field Strength
Bruker
DMX
500.0
Bruker
DMX
600.0
Bruker
DRX
800.0
NMR Refinement
Method
simulated annealing molecular dynamics in Cartesian space
Details
Structures were calculated in a three stage process. In the first stage, folds were calculated from a fully-extended chain based only on torsion and NOE restraints. In the second stage, the ten best structures of stage 1 were used as starting structures in a simulated annealing calculation that included dipolar restraints measured in bicelles. In the last stage, the ten lowest energy structures of Stage 2 were used as starting structures in a simulated annealing calculation that also included dipolar restraints measured in a phage liquid crystal.
NMR Ensemble Information
Conformer Selection Criteria
structures with the lowest energy
Conformers Calculated Total Number
30
Conformers Submitted Total Number
20
Additional NMR Experimental Information
1
This structure was determined using two sets of dipolar coupling restraints. One set was recorded in a bicelle liquid crystal solution; the other set was recorded in a phage liquid crystal solution. See citation 1 for details on solution conditions. A total of 127 N-H, 135 CA-HA, 138 CA-CO, 61 N-CO, and 64 CO-HN dipolar restraints were used in the structure calculation. Additional restraints included 592 intraresidue, 278 short range, 104 medium range, and 140 long range NOE restraints as well as 76 phi, 51 psi, and 21 chi1 dihedral restraints. A conformational database was employed in the simulated annealing calculation. No radius of gyration term was employed in the simulated annealing calculation.
Computation: NMR Software
#
Classification
Software Name
Author
1
processing
NMRPipe
Delaglio
2
data analysis
PIPP
Garrett
3
refinement
X-PLOR
Brunger
4
structure solution
X-PLOR
Brunger