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- PDB-1swr: CORE-STREPTAVIDIN MUTANT W120A IN COMPLEX WITH BIOTIN AT PH 7.5 -

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Basic information

Entry
Database: PDB / ID: 1swr
TitleCORE-STREPTAVIDIN MUTANT W120A IN COMPLEX WITH BIOTIN 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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6428
Polymers52,6654
Non-polymers9774
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11230 Å2
ΔGint-29 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.800, 99.900, 50.900
Angle α, β, γ (deg.)90.00, 112.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.690243, -0.568264, 0.44793), (-0.562579, 0.032156, -0.826118), (0.455049, -0.822218, -0.341888)12.7159, 3.1467, -4.7233
2given(-0.64211, 0.588439, 0.491359), (0.58052, -0.045388, 0.81298), (0.500691, 0.807267, -0.312457)25.5257, -27.5682, 14.092
3given(0.330626, -0.005136, -0.943748), (-0.018545, -0.999827, -0.001056), (-0.94358, 0.017851, -0.330664)17.3222, -23.7641, 24.5927
4given(0.335748, -0.020219, -0.941735), (-0.005227, -0.999794, 0.019602), (-0.941937, -0.001659, -0.335785)16.8911, -24.1693, 24.4747
5given(-0.647151, 0.587368, 0.485999), (0.574145, -0.043894, 0.817576), (0.50155, 0.808129, -0.308829)25.6406, -27.4054, 14.0123
6given(-0.686845, -0.576277, 0.442887), (-0.574336, 0.05692, -0.816638), (0.445401, -0.81527, -0.370072)12.503, 3.5598, -4.103

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Components

#1: Protein
CORE-STREPTAVIDIN


Mass: 13166.204 Da / Num. of mol.: 4 / Mutation: W120A
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.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.36 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-30 mg/mlprotein1drop
312-20 %PEG40001reservoir
40.1 MHEPES1reservoir
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: Dec 18, 1996
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: 30564 / % possible obs: 87 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.8 / % possible all: 74
Reflection
*PLUS
Num. measured all: 96477 / Rmerge(I) obs: 0.06

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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 1SWE

1swe


Resolution: 1.9→10 Å / Num. parameters: 15027 / Num. restraintsaints: 14976 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3077 10 %EVERY 10TH REFLECTION
all0.188 30564 --
obs0.184 -80.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3335 / Occupancy sum non hydrogen: 3756
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 64 207 3756
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.018
X-RAY DIFFRACTIONs_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.081
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.157 / Rfactor Rfree: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2

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