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- PDB-1swb: APO-CORE-STREPTAVIDIN AT PH 7.5 -

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Basic information

Entry
Database: PDB / ID: 1swb
TitleAPO-CORE-STREPTAVIDIN AT PH 7.5
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN / BIOTIN 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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 4, 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 1.3Aug 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

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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
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-53 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.900, 88.200, 47.400
Angle α, β, γ (deg.)90.00, 98.70, 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 7.5 / Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growpH: 4.5
Details: PROTEIN WAS CRYSTALLIZED FROM 48% MPD (2-METHYL-PENTANE-2,4-DIOLE, PH 4.5), 5.5H SOAKING IN 0.1M HEPES BUFFER PH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 mg/mlprotein1drop
248 %MPD1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: NICOLET / Detector: AREA DETECTOR / Date: Nov 28, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 30418 / % possible obs: 78 % / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 11
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 2 / % possible all: 48

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWA

1swa


Resolution: 1.85→10 Å / Num. parameters: 14851 / Num. restraintsaints: 14740 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2970 10 %EVERY 10TH REFLECTION
all0.174 30164 --
obs0.17 -74 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3279 / Occupancy sum non hydrogen: 3712
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 0 209 3712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.084
X-RAY DIFFRACTIONs_zero_chiral_vol0.095
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.084
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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