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- PDB-1swf: CIRCULAR PERMUTED STREPTAVIDIN E51/A46 -

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Basic information

Entry
Database: PDB / ID: 1swf
TitleCIRCULAR PERMUTED STREPTAVIDIN E51/A46
ComponentsCIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
KeywordsBIOTIN-BINDING PROTEIN / BIOTIN BINDING PROTEIN / CIRCULAR PERMUTATION / BIOTIN
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: 2 Å
AuthorsFreitag, S. / Chu, V. / Le Trong, I. / Stayton, P.S. / Stenkamp, R.E.
Citation
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.
#1: Journal: To be Published
Title: Thermodynamic Consequences of the Deletion of a Flexible Loop 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
DepositionApr 23, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 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: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
B: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
C: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
D: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46


Theoretical massNumber of molelcules
Total (without water)53,3184
Polymers53,3184
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-50 kcal/mol
Surface area20730 Å2
MethodPISA
2
A: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
B: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46

C: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
D: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46


Theoretical massNumber of molelcules
Total (without water)53,3184
Polymers53,3184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area8320 Å2
ΔGint-44 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.296, 78.596, 93.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.368327, 0.918525, -0.143669), (0.920717, -0.381815, -0.080607), (-0.128902, -0.102606, -0.986335)-21.2169, 42.1623, 72.3347
2given(-0.366917, -0.92739, 0.07294), (-0.921627, 0.351742, -0.163955), (0.126394, -0.127382, -0.983768)53.3859, 44.1947, 69.3494
3given(-0.999988, -0.002134, 0.004473), (0.003089, -0.974171, 0.22579), (0.003875, 0.225801, 0.974166)29.6755, 68.2432, -7.8404
4given(-0.999996, -0.00123, 0.00265), (0.001808, -0.973076, 0.230479), (0.002295, 0.230483, 0.973074)29.7336, 68.0573, -7.9372
5given(-0.366022, -0.926808, 0.083988), (-0.920074, 0.346863, -0.182073), (0.139615, -0.143918, -0.970692)53.0918, 45.0139, 69.6652
6given(0.364567, 0.927966, -0.077262), (0.927138, -0.369454, -0.062605), (-0.08664, -0.048809, -0.995043)-23.485, 40.8078, 69.8713

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Components

#1: Protein
CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46


Mass: 13329.403 Da / Num. of mol.: 4
Mutation: DELETION OF SURFACE LOOP RESIDUES 45 - 50 FROM THE SEQUENCE. THE OLD N- AND C-TERMINI (S139, A13, RESPECTIVELY) ARE CONNECTED INTRODUCING THE FOUR ADDITIONAL RESIDUES GGGS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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 Å3/Da / Density % sol: 40.79 %
Crystal growpH: 4.5 / Details: PROTEIN WAS CRYSTALLIZED FROM 52% MPD (PH 4.5).
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
252 %MPD1reservoir

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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: Jun 24, 1996 / Details: MSC MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 28795 / % possible obs: 94 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 5
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 82
Reflection
*PLUS
Num. measured all: 93577
Reflection shell
*PLUS
% possible obs: 82.1 %

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Processing

Software
NameClassification
SHELXL-96model building
X-PLORmodel building
SHELXL-96refinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWA (EXCLUDING RESIDUES 46 - 51 IN ALL SUBUNITS)

1swa


Resolution: 2→10 Å / Num. parameters: 15175 / Num. restraintsaints: 15088 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2860 10 %EVERY 10TH REFLECTION
all0.195 28548 --
obs0.19 -94 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3354 / Occupancy sum non hydrogen: 3790
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 0 214 3790
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_planes0.048
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.011
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.09
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
σ(I): 2 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2

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