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- PDB-1swk: CORE-STREPTAVIDIN MUTANT W79F IN COMPLEX WITH BIOTIN AT PH 4.5 -

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Basic information

Entry
Database: PDB / ID: 1swk
TitleCORE-STREPTAVIDIN MUTANT W79F IN COMPLEX WITH BIOTIN AT PH 4.5
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
BIOTIN / EPI-BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 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 24, 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
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)53,9468
Polymers52,9694
Non-polymers9774
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-38 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.300, 64.600, 76.000
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.994808, 0.024259, -0.098834), (0.03204, -0.847124, -0.530428), (-0.096593, -0.530841, 0.841949)31.6975, 24.1472, 8.6658
2given(0.99386, 0.022179, 0.108399), (0.021695, -0.999749, 0.005648), (0.108497, -0.003261, -0.994091)-2.0759, 15.7492, 34.7372
3given(-0.998498, -0.053667, -0.011057), (-0.051325, 0.845392, 0.531675), (-0.019185, 0.531444, -0.846876)30.7898, -7.6479, 29.6087
4given(-0.998459, -0.052244, -0.018699), (-0.054165, 0.844445, 0.532896), (-0.012051, 0.533088, -0.845974)30.9011, -7.655, 29.4834
5given(0.993523, 0.029435, 0.109757), (0.029133, -0.999566, 0.004356), (0.109837, -0.00113, -0.993949)-2.1365, 15.7, 34.6307
6given(-0.995583, 0.023029, -0.091018), (0.029547, -0.84334, -0.536567), (-0.089115, -0.536886, 0.838935)31.5647, 24.2303, 8.6692

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Components

#1: Protein
CORE-STREPTAVIDIN


Mass: 13242.300 Da / Num. of mol.: 4 / Mutation: W79F
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


Mass: 244.311 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Chemical ChemComp-BTQ / EPI-BIOTIN / 5-[(3AS,4R,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANOIC ACID


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.74 Å3/Da / Density % sol: 55.17 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-30 mg/mlprotein1drop
248 %MPD1reservoir
3biotin1drop2.5 molar excess

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 30, 1996 / Details: MSC MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→43.1 Å / Num. obs: 38017 / % possible obs: 97 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.9
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.7 / % possible all: 87
Reflection
*PLUS
Num. measured all: 38347
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

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

1swa


Resolution: 2→10 Å / Num. parameters: 15071 / Num. restraintsaints: 14952 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3782 10 %EVERY 10TH REFLECTION
all0.186 38107 --
obs0.184 -97 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3264 / Occupancy sum non hydrogen: 3767
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 64 221 3773
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.017
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.079
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.221 / Rfactor obs: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 0.025

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