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- PDB-1swp: CORE-STREPTAVIDIN MUTANT W120F IN COMPLEX WITH BIOTIN AT PH 7.5 -

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Basic information

Entry
Database: PDB / ID: 1swp
TitleCORE-STREPTAVIDIN MUTANT W120F 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 / 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 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

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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
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-36 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.800, 100.000, 51.800
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.685799, -0.570861, 0.451439), (-0.570851, 0.037161, -0.820212), (0.451451, -0.820206, -0.351362)13.1157, 3.831, -4.0509
2given(-0.644666, 0.586632, 0.490172), (0.579551, -0.043098, 0.813796), (0.498524, 0.808706, -0.312199)25.8629, -28.2584, 14.2508
3given(0.329407, -0.008588, -0.944149), (-0.011025, -0.999925, 0.005248), (-0.944124, 0.00868, -0.329477)17.7768, -23.9264, 25.2373
4given(0.328547, -0.012243, -0.944408), (-0.005479, -0.999924, 0.011057), (-0.944472, 0.001541, -0.328589)17.6684, -24.1188, 25.1526
5given(-0.645822, 0.585948, 0.489468), (0.580625, -0.039363, 0.813219), (0.495771, 0.809392, -0.314795)25.8108, -27.9693, 14.1958
6given(-0.681617, -0.576768, 0.450263), (-0.576952, 0.045181, -0.815528), (0.450027, -0.815657, -0.363564)12.7377, 3.6134, -4.1155

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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: 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.: 185 / 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: 2.43 Å3/Da / Density % sol: 49 %
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: Nov 13, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 24596 / % possible obs: 90 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.9
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.5 / % possible all: 75
Reflection
*PLUS
Num. measured all: 62223
Reflection shell
*PLUS
% possible obs: 75 %

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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: 2→10 Å / Num. parameters: 14951 / Num. restraintsaints: 27450 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: NON CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE APPLIED FOR THE FOUR SUBUNITS OF THE TETRAMER
RfactorNum. reflection% reflectionSelection details
Rfree0.329 2433 10 %EVERY 10TH REFLECTION
all0.255 24289 --
obs0.251 -76 %-
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: 3737
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 64 185 3737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0.046
X-RAY DIFFRACTIONs_from_restr_planes0.015
X-RAY DIFFRACTIONs_zero_chiral_vol0.072
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.017
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.029
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 24596 / Rfactor all: 0.202 / Rfactor Rfree: 0.278
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.015

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