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- PDB-1nqm: Structure of Savm-W120K, streptavidin mutant -

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Basic information

Entry
Database: PDB / ID: 1nqm
TitleStructure of Savm-W120K, streptavidin mutant
ComponentsStreptavidin
KeywordsUNKNOWN FUNCTION / avidin / streptavidin / biotin / monomer-monomer interaction / high affinity systems
Function / homology
Function and homology information


biotin binding / 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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPazy, Y. / Eisenberg-Domovich, Y. / Laitinen, O.H. / Kulomaa, M.S. / Bayer, E.A. / Wilchek, M. / Livnah, O.
CitationJournal: J.Bacteriol. / Year: 2003
Title: Dimer-Tetramer Transition between Solution and Crystalline States of Streptavidin and Avidin Mutants.
Authors: Pazy, Y. / Eisenberg-Domovich, Y. / Laitinen, O.H. / Kulomaa, M.S. / Bayer, E.A. / Wilchek, M. / Livnah, O.
History
DepositionJan 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7598
Polymers56,7814
Non-polymers9774
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-34 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.433, 100.407, 52.511
Angle α, β, γ (deg.)90.00, 112.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin


Mass: 14195.374 Da / Num. of mol.: 4 / Mutation: W120K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Cell line (production host): JM109 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P22629
#2: Chemical
ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.45
Details: 25% PEG 6K, 0.3M sodium acetate, 0.1M cac. buffer, pH 6.45, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
215 %PEG80001reservoir
30.2 Msodium acetate1reservoir
40.1 Msodium cacodylate1reservoirpH6.45

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Num. obs: 51529 / % possible obs: 97.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 2467 RANDOM
Rwork0.212 --
all0.215 53164 -
obs0.214 49242 -
Refinement stepCycle: LAST / Resolution: 1.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 64 223 3813
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.01
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.6

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