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

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Basic information

Entry
Database: PDB / ID: 1swc
TitleAPO-CORE-STREPTAVIDIN AT PH 4.5
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 ...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: 1.8 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
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: STREPTAVIDIN
B: STREPTAVIDIN
C: STREPTAVIDIN
D: STREPTAVIDIN


Theoretical massNumber of molelcules
Total (without water)53,1254
Polymers53,1254
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-51 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.800, 65.900, 82.100
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.92292, -0.287451, 0.256106), (-0.281911, 0.051549, -0.958055), (0.262192, -0.956407, -0.128611)-9.4391, 32.9108, 38.9042
2given(-0.034131, 0.812991, 0.581275), (0.79669, -0.329032, 0.506974), (0.603423, 0.480399, -0.636472)-28.9849, 14.3203, 28.2587
3given(-0.041395, -0.528401, -0.847985), (-0.53247, -0.706481, 0.466219), (-0.845436, 0.470825, -0.252113)20.5396, 14.781, 14.0443
4given(-0.034887, -0.526218, -0.849633), (-0.531619, -0.71012, 0.46164), (-0.846265, 0.467787, -0.254974)20.5671, 14.8882, 14.0103
5given(-0.033348, 0.793029, 0.608271), (0.810293, -0.334828, 0.480953), (0.585076, 0.508916, -0.631419)-29.43, 14.7372, 27.6063
6given(-0.932951, -0.26461, 0.2441), (-0.260718, 0.029048, -0.964978), (0.248252, -0.963918, -0.096089)-9.7223, 33.1866, 38.1977

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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.: 226 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growpH: 4.5
Details: PROTEIN WAS CRYSTALLIZED FROM 60% MPD (2-METHYL-PENTANE-2,4-DIOLE, PH 4.5), SOAKING IN 20 MM SODIUM ACETATE BUFFER 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
260 %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: Jan 4, 1994 / Details: MSC MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→43.46 Å / Num. obs: 48224 / % possible obs: 79 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 3.3 / % possible all: 48

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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: PDB ENTRY 1SWA

1swa


Resolution: 1.8→10 Å / Num. parameters: 14775 / Num. restraintsaints: 14645 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3738 10 %EVERY 10TH REFLECTION
all0.163 37350 --
obs0.159 -79 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3230 / Occupancy sum non hydrogen: 3690
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3464 0 0 226 3690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.019
X-RAY DIFFRACTIONs_zero_chiral_vol0.107
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.117
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.088
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS

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