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- PDB-1swn: CORE-STREPTAVIDIN MUTANT W108F IN COMPLEX WITH BIOTIN AT PH 7.0 -

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Basic information

Entry
Database: PDB / ID: 1swn
TitleCORE-STREPTAVIDIN MUTANT W108F IN COMPLEX WITH BIOTIN AT PH 7.0
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7027
Polymers52,9694
Non-polymers7333
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10750 Å2
ΔGint-40 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.600, 88.700, 48.000
Angle α, β, γ (deg.)90.00, 98.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.00136, 0.950731, 0.310015), (0.951321, -0.094317, 0.293416), (0.308199, 0.295323, -0.904322)8.7067, -15.7944, 20.3373
2given(-0.00581, -0.950961, -0.309257), (-0.951517, -0.089855, 0.294178), (-0.30754, 0.295973, -0.904333)15.4878, 7.328, 27.8559
3given(-0.999997, -0.002391, 0.000674), (0.00155, -0.812422, -0.583068), (0.001941, -0.583065, 0.812423)24.0327, 6.5551, 2.1585
4given(-0.999974, -0.007168, -0.001176), (0.006492, -0.809259, -0.587416), (0.003259, -0.587408, 0.809284)24.1679, 6.4454, 2.1126
5given(0.003407, -0.950309, -0.311291), (-0.952563, -0.097818, 0.288193), (-0.304322, 0.295542, -0.905562)15.3271, 7.5938, 27.7905
6given(0.003732, 0.952906, 0.303242), (0.951947, -0.096251, 0.290745), (0.30624, 0.287585, -0.907475)8.4468, -15.4935, 20.4532

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Components

#1: Protein
CORE-STREPTAVIDIN


Mass: 13242.301 Da / Num. of mol.: 4 / Mutation: W108F
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: Chemical ChemComp-BTN / BIOTIN / Biotin


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


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-30 mg/mlprotein1drop
322-24 %PEG10001reservoir
40.1 MTris-HCl1reservoir
2biotin1drop2.5 molar excess

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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: Nov 21, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 19696 / % possible obs: 87 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.8
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / % possible all: 35
Reflection
*PLUS
Num. measured all: 84710

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Processing

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

1swa


Resolution: 2.2→10 Å / Num. parameters: 14999 / Num. restraintsaints: 14914 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: LOOP RESIDUES 45-48 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. LOOP RESIDUES 45-52 WERE REFINED WITH AN OCCUPANCY OF 0.5 IN CHAIN C.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1943 10 %EVERY 10TH REFLECTION
all0.181 19403 --
obs0.178 -81 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3315.5 / Occupancy sum non hydrogen: 3716
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 0 48 192 3750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.015
X-RAY DIFFRACTIONs_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.16 / Rfactor Rfree: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.015

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