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- PDB-1swa: APO-CORE-STREPTAVIDIN AT PH 4.5 -

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Basic information

Entry
Database: PDB / ID: 1swa
TitleAPO-CORE-STREPTAVIDIN AT PH 4.5
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN / 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: 1.9 Å
AuthorsFreitag, S. / Le Trong, I. / Klumb, L. / Stayton, P.S. / Stenkamp, R.E.
CitationJournal: 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
DepositionMar 2, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
C: STREPTAVIDIN
D: STREPTAVIDIN


Theoretical massNumber of molelcules
Total (without water)53,1254
Polymers53,1254
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-49 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.500, 87.100, 47.000
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.002566, 0.948069, 0.318056), (0.948056, -0.098865, 0.302349), (0.318093, 0.302311, -0.898568)8.278, -15.4751, 20.0502
2given(-0.001481, -0.950853, -0.309638), (-0.949464, -0.09585, 0.298883), (-0.313873, 0.294433, -0.902659)15.4755, 7.0511, 27.5857
3given(-0.99997, 0.007252, -0.002739), (-0.004176, -0.801647, -0.597784), (-0.006531, -0.597754, 0.801653)23.7301, 6.9094, 2.2834
4given(-0.999982, 0.005196, -0.002993), (-0.002389, -0.803001, -0.595972), (-0.0055, -0.595955, 0.802999)23.7346, 6.8746, 2.3288
5given(-0.003465, -0.949612, -0.31341), (-0.950165, -0.094573, 0.297056), (-0.311728, 0.29882, -0.90196)15.4286, 7.2121, 27.6666
6given(0.007521, 0.949291, 0.314309), (0.948741, -0.106091, 0.297716), (0.315964, 0.295959, -0.901429)8.0882, -15.2981, 20.2216

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Components

#1: Protein
STREPTAVIDIN / CORE STREPTAVIDIN


Mass: 13281.336 Da / Num. of mol.: 4 / Fragment: CORE, RESIDUES 13 - 139
Source method: isolated from a genetically manipulated source
Details: PH 4.5 / 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.: 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growpH: 4.5 / Details: PROTEIN WAS CRYSTALLIZED FROM 47% MPD (PH 4.5)
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 mg/mlprotein1drop
247 %MPD1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 11, 1994 / Details: MSC MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→43.54 Å / Num. obs: 26574 / % possible obs: 79 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.049 / Net I/σ(I): 9
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 2.5 / % possible all: 28

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Processing

Software
NameClassification
SHELXL-96model building
X-PLORmodel building
SHELXL-96refinement
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
SHELXL-96phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NOT PUBLISHED YET, STREPTAVIDIN MUTANT STRUCTURE

Resolution: 1.9→10 Å / Num. parameters: 14871 / Num. restraintsaints: 14821 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2607 10 %EVERY 10TH REFLECTION
all0.154 26341 --
obs0.147 -72 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3279 / Occupancy sum non hydrogen: 3714
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 0 211 3714
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_vol0.097
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.144
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS

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