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- PDB-3ry1: Wild-type core streptavidin at atomic resolution -

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Basic information

Entry
Database: PDB / ID: 3ry1
TitleWild-type core streptavidin at atomic resolution
ComponentsStreptavidin
KeywordsBiotin-binding protein
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
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous to previous structure / Resolution: 1.03 Å
AuthorsStenkamp, R.E. / Wang, Z. / Le Trong, I. / Stayton, P.S. / Lybrand, T.P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Streptavidin and its biotin complex at atomic resolution.
Authors: Le Trong, I. / Wang, Z. / Hyre, D.E. / Lybrand, T.P. / Stayton, P.S. / Stenkamp, R.E.
History
DepositionMay 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)54,30714
Polymers53,1254
Non-polymers1,18210
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-75 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.018, 84.432, 45.994
Angle α, β, γ (deg.)90.00, 98.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin


Mass: 13281.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P22629
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 52% MPD, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.03→47.46 Å / Num. all: 206004 / Num. obs: 206004 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.037 / Χ2: 0.955 / Net I/σ(I): 27.227
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.03-1.050.222105441.091199.8
1.05-1.070.166105450.8991100
1.07-1.090.137105250.911100
1.09-1.110.111105540.9181100
1.11-1.130.099105790.926199.8
1.13-1.160.087104670.927199.1
1.16-1.190.08103080.922197.6
1.19-1.220.078102470.927196.9
1.22-1.250.074101430.925196.5
1.25-1.290.067101780.907196.2
1.29-1.330.061101621.008196.2
1.33-1.390.055102150.995196.5
1.39-1.450.049102730.99197
1.45-1.520.042103100.984197.6
1.52-1.610.038104060.988198.3
1.61-1.720.034104970.983199.2
1.72-1.880.03105860.969199.6
1.88-2.120.028105700.97199.7
2.121-2.550.027106050.945199.6
2.552-40.02882900.931177.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
Fccalculationphasing
RefinementMethod to determine structure: Isomorphous to previous structure
Resolution: 1.03→47.46 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.1323 / WRfactor Rwork: 0.113 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9427 / SU B: 0.513 / SU ML: 0.012 / SU R Cruickshank DPI: 0.0221 / SU Rfree: 0.0225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.135 10472 5 %RANDOM
Rwork0.1169 ---
all0.1178 209009 --
obs0.1178 198537 95.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.04 Å2 / Biso mean: 13.428 Å2 / Biso min: 4.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.04 Å2
2--0.36 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.03→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 80 576 4281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214399
X-RAY DIFFRACTIONr_bond_other_d0.0020.022716
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9246135
X-RAY DIFFRACTIONr_angle_other_deg1.25736693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6545634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.32123.837172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00315613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0781519
X-RAY DIFFRACTIONr_chiral_restr0.2810.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025136
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02943
X-RAY DIFFRACTIONr_mcbond_it2.64842750
X-RAY DIFFRACTIONr_mcbond_other2.70141159
X-RAY DIFFRACTIONr_mcangle_it3.66264461
X-RAY DIFFRACTIONr_scbond_it3.78461649
X-RAY DIFFRACTIONr_scangle_it5.002101630
X-RAY DIFFRACTIONr_rigid_bond_restr1.96737115
X-RAY DIFFRACTIONr_sphericity_free10.0353636
X-RAY DIFFRACTIONr_sphericity_bonded5.66236967
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.164 793 -
Rwork0.144 15052 -
all-15845 -
obs--99.87 %

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