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- PDB-2klw: Solution structure of an abc collagen heterotrimer reveals a sing... -

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Basic information

Entry
Database: PDB / ID: 2klw
TitleSolution structure of an abc collagen heterotrimer reveals a single-register helix stabilized by electrostatic interactions
Components
  • (DOG)10
  • (PKG)10
  • (POG)10
KeywordsDE NOVO PROTEIN / Collagen / Synthetic Peptide / Heterotrimer
MethodSOLUTION NMR / simulated annealing, constraint minimization
Model detailslowest energy, model 1
AuthorsFallas, J.A. / Gauba, V. / Hartgerink, J.D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Solution structure of an ABC collagen heterotrimer reveals a single-register helix stabilized by electrostatic interactions.
Authors: Fallas, J.A. / Gauba, V. / Hartgerink, J.D.
History
DepositionJul 9, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (PKG)10
B: (DOG)10
C: (POG)10


Theoretical massNumber of molelcules
Total (without water)8,4853
Polymers8,4853
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide (PKG)10


Mass: 2875.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fmoc based solid phase peptide synthesis
#2: Protein/peptide (DOG)10


Mass: 2894.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fmoc based solid phase peptide synthesis
#3: Protein/peptide (POG)10


Mass: 2714.874 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fmoc based solid phase peptide synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1322D 1H-1H TOCSY
1432D 1H-1H TOCSY
1542D 1H-1H TOCSY
1642D 1H-1H NOESY
1752D 1H-13C HSQC
1852D 1H-15N HSQC
1953D HNHA
11052D 1H-1H 13C-HMQC NOESY 15N-HSQC
21112D 1H-1H NOESY
21212D 1H-1H TOCSY
11362D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2 mM K-1, 1.2 mM D-2, 1.2 mM O-3, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM K-4, 90% H2O/10% D2O90% H2O/10% D2O
31.2 mM D-5, 90% H2O/10% D2O90% H2O/10% D2O
41.2 mM O-6, 90% H2O/10% D2O90% H2O/10% D2O
51.2 mM [U-99% 13C; U-99% 15N] K-7, 1.2 mM [U-99% 13C; U-99% 15N] D-8, 1.2 mM [U-99% 13C; U-99% 15N] O-9, 90% H2O/10% D2O90% H2O/10% D2O
61.8 mM K-10, 1.2 mM D-11, 1.2 mM O-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMK-11
1.2 mMD-21
1.2 mMO-31
1.2 mMK-42
1.2 mMD-53
1.2 mMO-64
1.2 mMK-7[U-99% 13C; U-99% 15N]5
1.2 mMD-8[U-99% 13C; U-99% 15N]5
1.2 mMO-9[U-99% 13C; U-99% 15N]5
1.8 mMK-106
1.2 mMD-116
1.2 mMO-126
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 298 K
27ambient 283 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSv 1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
SparkyGoddardchemical shift assignment
Amber9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CcpNMRCCPNdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing, constraint minimization / Software ordinal: 1
Details: simulated annealing in CNS using a combination of torsional and cartesian dynamics, refinement in implicit solvent using amber
NMR constraintsNOE constraints total: 771 / NOE intraresidue total count: 253 / NOE long range total count: 0 / NOE medium range total count: 0 / NOE sequential total count: 180 / Protein chi angle constraints total count: 48 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 72 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 1.86 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 15 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.25 Å
NMR ensemble rmsDistance rms dev: 0.1 Å / Distance rms dev error: 0.01 Å

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