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- PDB-2bc3: T7-tagged full-length streptavidin -

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Basic information

Entry
Database: PDB / ID: 2bc3
TitleT7-tagged full-length streptavidin
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / streptavidin / T7 tag
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
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsStenkamp, R.E. / Le Trong, I. / Ward, T.R. / Humbert, N.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystallographic Analysis of a Full-length Streptavidin with Its C-terminal Polypeptide Bound in the Biotin Binding Site.
Authors: Le Trong, I. / Humbert, N. / Ward, T.R. / Stenkamp, R.E.
History
DepositionOct 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 21, 2022Group: 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 1.4Apr 3, 2024Group: 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

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4205
Polymers33,1402
Non-polymers2803
Water5,026279
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,84110
Polymers66,2804
Non-polymers5616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area11750 Å2
ΔGint-77 kcal/mol
Surface area21340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.704, 82.391, 46.710
Angle α, β, γ (deg.)90.00, 103.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-5001-

SO4

21A-6119-

HOH

31A-6160-

HOH

41B-6120-

HOH

51B-6129-

HOH

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Components

#1: Protein Streptavidin


Mass: 16570.018 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pET11b / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.12 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 25% Ammonium Sulfate, 0.1M NaAcetate pH4.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.541781
ReflectionResolution: 1.53→50 Å / Num. obs: 35381 / % possible obs: 77.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.1
Reflection shellResolution: 1.53→1.58 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.9 / Num. unique all: 318 / % possible all: 7.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: streptavidin monomer

Resolution: 1.54→10 Å / Num. parameters: 9763 / Num. restraintsaints: 6886 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 3521 10 %RANDOM
Rwork0.175 ---
all0.1794 35214 --
obs0.1753 35214 79.7 %-
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 1866.5 / Occupancy sum non hydrogen: 2353.5
Refinement stepCycle: LAST / Resolution: 1.54→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 15 279 2405
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0287
X-RAY DIFFRACTIONs_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.057
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.157
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0

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