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- PDB-1ndj: Streptavidin Mutant Y43F with Biotin at 1.81A Resolution -

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Basic information

Entry
Database: PDB / ID: 1ndj
TitleStreptavidin Mutant Y43F with Biotin at 1.81A Resolution
ComponentsStreptavidin
KeywordsBIOTIN-BINDING PROTEIN / tetramer
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 ...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 / ISOMORPHOUS / Resolution: 1.81 Å
AuthorsLe Trong, I. / Freitag, S. / Klumb, L.A. / Chu, V. / Stayton, P.S. / Stenkamp, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural studies of hydrogen bonds in the high-affinity streptavidin-biotin complex: mutations of amino acids interacting with the ureido oxygen of biotin.
Authors: Le Trong, I. / Freitag, S. / Klumb, L.A. / Chu, V. / Stayton, P.S. / Stenkamp, R.E.
History
DepositionDec 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)54,0398
Polymers53,0614
Non-polymers9774
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-39 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.300, 98.400, 52.800
Angle α, β, γ (deg.)90.00, 112.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin


Mass: 13265.336 Da / Num. of mol.: 4 / Fragment: core streptavidin, residues 13-139 / Mutation: Y43F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Gene: core streptavidin / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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.: 229 / 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: 1.93 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-30 mg/mlprotein1drop
216 %PEG40001reservoir
30.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.81→99 Å / Num. all: 35211 / Num. obs: 35211 / % possible obs: 79.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 1.8 Å / % possible obs: 80 % / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 30 % / Rmerge(I) obs: 0.32

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementMethod to determine structure: ISOMORPHOUS
Starting model: 1SWE

1swe


Resolution: 1.81→10 Å / Num. parameters: 15159 / Num. restraintsaints: 15067 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.312 3500 10 %RANDOM
Rwork0.222 ---
all0.2273 35008 --
obs0.2273 35008 80.7 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3328 / Occupancy sum non hydrogen: 3789
Refinement stepCycle: LAST / Resolution: 1.81→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 64 229 3789
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0275
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.077
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS

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