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- PDB-2mf6: Solution NMR structure of Chimeric Avidin, ChiAVD(I117Y), in the ... -

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Basic information

Entry
Database: PDB / ID: 2mf6
TitleSolution NMR structure of Chimeric Avidin, ChiAVD(I117Y), in the biotin bound form
ComponentsAvidin, Avidin-related protein 4/5
KeywordsBIOTIN BINDING PROTEIN
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Avidin / Avidin-related protein 4/5
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsTossavainen, H. / Kukkurainen, S. / Maatta, J.A.E. / Pihlajamaa, T. / Hytonen, V.P. / Kulomaa, M.S. / Permi, P.
CitationJournal: Plos One / Year: 2014
Title: Chimeric Avidin - NMR Structure and Dynamics of a 56 kDa Homotetrameric Thermostable Protein
Authors: Tossavainen, H. / Kukkurainen, S. / Maatta, J.A.E. / Kahkonen, N. / Pihlajamaa, T. / Hytonen, V.P. / Kulomaa, M.S. / Permi, P.
History
DepositionOct 7, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avidin, Avidin-related protein 4/5
D: Avidin, Avidin-related protein 4/5
B: Avidin, Avidin-related protein 4/5
C: Avidin, Avidin-related protein 4/5


Theoretical massNumber of molelcules
Total (without water)57,6014
Polymers57,6014
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein
Avidin, Avidin-related protein 4/5 /


Mass: 14400.254 Da / Num. of mol.: 4
Fragment: P02701 Residues 25-61, 85-152 and P56734 residues 62-82
Mutation: I117Y
Source method: isolated from a genetically manipulated source
Details: chimera of Avidin and Avidin-related protein 4/5 / Source: (gene. exp.) Gallus gallus (chicken) / Gene: AVD, AVR4, AVR5 / Production host: Escherichia coli (E. coli) / References: UniProt: P02701, UniProt: P56734
Sequence detailsTHIS ENTRY IS A CHIMERA OF AVIDIN AND AVIDIN-RELATED PROTEIN 4/5.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D H(CCO)NH
1613D C(CO)NH
1713D (H)CCH-COSY
181(HB)CB(CGCD)HD
191HCCmHm
11013D 1H-13C NOESY
11113D 1H-15N NOESY
21223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7-1.2 mM [U-13C; U-15N] avidin-1, 0.7-1.2 mM d-biotin-2, 93 % H2O-3, 7 % D2O-4, 93% H2O/7% D2O93% H2O/7% D2O
20.7-1.2 mM [U-13C; U-15N] avidin-5, 0.7-1.2 mM d-biotin-6, 100 % D2O-7, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMavidin-1[U-13C; U-15N]0.7-1.21
mMd-biotin-20.7-1.21
93 %H2O-31
7 %D2O-41
mMavidin-5[U-13C; U-15N]0.7-1.22
mMd-biotin-60.7-1.22
100 %D2O-72
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.5 1 atm333 K
26.5 1 atm333 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
VNMRVarianprocessing
SparkyGoddard, Guntert, Mumenthaler and Wuthrichdata analysis
SparkyGoddard, Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
X-PLOR NIHrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15 / Representative conformer: 1

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