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- PDB-1swo: CORE-STREPTAVIDIN MUTANT W120F AT PH 7.5 -

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Basic information

Entry
Database: PDB / ID: 1swo
TitleCORE-STREPTAVIDIN MUTANT W120F AT PH 7.5
ComponentsCORE-STREPTAVIDIN
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFreitag, S. / Le Trong, I. / Chilkoti, A. / Klumb, L.A. / Stayton, P.S. / Stenkamp, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structural studies of binding site tryptophan mutants in the high-affinity streptavidin-biotin complex.
Authors: Freitag, S. / Le Trong, I. / Chilkoti, A. / Klumb, L.A. / Stayton, P.S. / Stenkamp, R.E.
#1: Journal: Protein Sci. / Year: 1998
Title: Thermodynamic and Structural Consequences of Flexible Loop Deletion by Circular Permutation in the Streptavidin-Biotin System
Authors: Chu, V. / Freitag, S. / Le Trong, I. / Stenkamp, R.E. / Stayton, P.S.
#2: Journal: Protein Sci. / Year: 1997
Title: Structural Studies of the Streptavidin Binding Loop
Authors: Freitag, S. / Le Trong, I. / Klumb, L. / Stayton, P.S. / Stenkamp, R.E.
History
DepositionJan 27, 1998Processing site: BNL
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Other
Category: database_2 / pdbx_database_status / 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.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 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: CORE-STREPTAVIDIN
B: CORE-STREPTAVIDIN
C: CORE-STREPTAVIDIN
D: CORE-STREPTAVIDIN


Theoretical massNumber of molelcules
Total (without water)52,9694
Polymers52,9694
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-50 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 87.200, 47.100
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.010435, 0.947855, 0.318532), (0.948185, -0.091781, 0.304173), (0.317547, 0.305202, -0.897784)8.5398, -15.6676, 19.9574
2given(0.001244, -0.949466, -0.313867), (-0.949279, -0.099811, 0.298174), (-0.314434, 0.297577, -0.901432)15.2084, 7.1163, 27.5773
3given(-0.999924, 0.012183, -0.001686), (-0.00873, -0.799584, -0.600491), (-0.008664, -0.60043, 0.79963)23.7896, 6.7504, 2.2547
4given(-0.99995, -0.007486, -0.006606), (0.009953, -0.799607, -0.600441), (-0.000787, -0.600477, 0.799642)23.8308, 6.5242, 2.2391
5given(-0.000586, -0.949638, -0.313348), (-0.948942, -0.098318, 0.299739), (-0.315451, 0.297524, -0.901094)15.2903, 7.1098, 27.6438
6given(0.00975, 0.94765, 0.319163), (0.947491, -0.11078, 0.29998), (0.319632, 0.299479, -0.89897)8.1211, -15.4681, 20.0732

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Components

#1: Protein
CORE-STREPTAVIDIN


Mass: 13242.301 Da / Num. of mol.: 4 / Mutation: W120F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Description: PET-210, NOVAGEN, INC., MADISON,WI / Plasmid: PET-210 / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.25 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120-30 mg/mlprotein1drop
212-20 %PEG40001reservoir
30.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 17, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2 Å / Num. obs: 26060 / % possible obs: 82 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.042 / Net I/σ(I): 18.7
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.114 / Mean I/σ(I) obs: 4.99 / % possible all: 56
Reflection
*PLUS
% possible obs: 78 % / Num. measured all: 53049 / Rmerge(I) obs: 0.04

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Processing

Software
NameClassification
SHELXL-97model building
X-PLORmodel building
SHELXL-97refinement
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
SHELXL-97phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWA

1swa


Resolution: 1.95→10 Å / Num. parameters: 14851 / Num. restraintsaints: 14626 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2661 10 %EVERY 10TH REFLECTION
all0.179 26615 --
obs0.175 -78 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3275 / Occupancy sum non hydrogen: 3712
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3484 0 0 228 3712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.016
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166 / Rfactor Rfree: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26 Å2

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