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- PDB-1swg: CIRCULAR PERMUTED STREPTAVIDIN E51/A46 IN COMPLEX WITH BIOTIN -

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Basic information

Entry
Database: PDB / ID: 1swg
TitleCIRCULAR PERMUTED STREPTAVIDIN E51/A46 IN COMPLEX WITH BIOTIN
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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionJul 12, 1997Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 1.4May 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: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2958
Polymers53,3184
Non-polymers9774
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
B: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1474
Polymers26,6592
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-16 kcal/mol
Surface area11020 Å2
MethodPISA, PQS
3
C: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
D: CIRCULARLY PERMUTED CORE-STREPTAVIDIN E51/A46
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1474
Polymers26,6592
Non-polymers4892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-15 kcal/mol
Surface area11480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.900, 78.600, 90.800
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(0.083893, 0.873313, -0.479882), (0.875098, -0.294911, -0.383708), (-0.476619, -0.387753, -0.788975)6.7883, 29.9289, 70.0848
2given(-0.152377, -0.632349, 0.75955), (-0.630602, -0.529552, -0.567376), (0.761001, -0.565429, -0.318069)20.1505, 71.9795, 37.2759
3given(-0.926623, -0.245959, -0.284382), (-0.243467, -0.18386, 0.952323), (-0.286519, 0.951682, 0.110486)53.5869, 12.3287, 3.3016
4given(-0.92817, -0.24112, -0.283482), (-0.245869, -0.174523, 0.953462), (-0.279373, 0.954674, 0.102703)53.423, 12.0844, 3.228
5given(-0.15421, -0.635123, 0.75686), (-0.626321, -0.529614, -0.572041), (0.76416, -0.562252, -0.316119)20.3536, 71.9558, 36.9848
6given(0.07751, 0.876585, -0.474965), (0.875822, -0.287493, -0.387665), (-0.476371, -0.385937, -0.790015)6.698, 29.7857, 70.0349

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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: 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.: 335 / 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: 2.4 Å3/Da / Density % sol: 48.87 %
Crystal growpH: 4.5
Details: PROTEIN (12MG/ML, 10MM BIOTIN) 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
112 mg/mlprotein1drop
210 mMbiotin1drop
352 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 / Details: RH-COATED SILICON MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 51393 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 19.9
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2 / % possible all: 87
Reflection
*PLUS
% possible obs: 98.2 % / Num. measured all: 417564 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.17

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWA (EXCLUDING RESIDUES 46 - 51 IN ALL SUBUNITS)

1swa


Resolution: 1.8→10 Å / Num. parameters: 15527 / Num. restraintsaints: 17457 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4748 10 %EVERY 10TH REFLECTION
all0.192 47484 --
obs0.19 -98 %-
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: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3461 0 64 335 3860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.025
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.016
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.051
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.073
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.231 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27 Å2

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