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- PDB-1g9e: SOLUTION STRUCTURE AND RELAXATION MEASUREMENTS OF AN ANTIGEN-FREE... -

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Entry
Database: PDB / ID: 1g9e
TitleSOLUTION STRUCTURE AND RELAXATION MEASUREMENTS OF AN ANTIGEN-FREE HEAVY CHAIN VARIABLE DOMAIN (VHH) FROM LLAMA
ComponentsH14
KeywordsIMMUNE SYSTEM / BETA BARREL
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesLama glama (llama)
MethodSOLUTION NMR / distance geometry, molecular dynamics
AuthorsRenisio, J.-G. / Perez, J. / Czisch, M. / Guenneugues, M. / Bornet, O. / Frenken, L. / Cambillau, C. / Darbon, H.
CitationJournal: Proteins / Year: 2002
Title: Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama
Authors: Renisio, J.-G. / Perez, J. / Czisch, M. / Guenneugues, M. / Bornet, O. / Frenken, L. / Cambillau, C. / Darbon, H.
History
DepositionNov 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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Assembly

Deposited unit
A: H14


Theoretical massNumber of molelcules
Total (without water)12,5221
Polymers12,5221
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)20 / 50Structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Antibody H14


Mass: 12521.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 4165492
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY

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Sample preparation

DetailsContents: 3mM 15N H14; 10mM deuterated Na acetate pH4.6 / Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4.6 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
UXNMR2.6BRUKERcollection
UXNMR2.6BRUKERprocessing
XEASY1.3.13Bartelsdata analysis
DIANA2.8Guntertstructure solution
CNS1Brungerrefinement
RefinementMethod: distance geometry, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 1295 restraints, 1181 are NOE-derived distance constraints, 57 dihedral angle restraints, 51 distance restraints from hydrogen bonds and 6 from the disulfide bridge.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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