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- PDB-1sws: CORE-STREPTAVIDIN MUTANT D128A AT PH 4.5 -

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Basic information

Entry
Database: PDB / ID: 1sws
TitleCORE-STREPTAVIDIN MUTANT D128A AT PH 4.5
ComponentsPROTEIN (STREPTAVIDIN)
KeywordsBINDING PROTEIN / BIOTIN BINDING PROTEIN
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
Streptavidin / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFreitag, S. / Chu, V. / Le Trong, I. / Klumb, L.A. / To, R. / Stayton, P.S. / Stenkamp, R.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: A structural snapshot of an intermediate on the streptavidin-biotin dissociation pathway.
Authors: Freitag, S. / Chu, V. / Penzotti, J.E. / Klumb, L.A. / To, R. / Hyre, D. / Le Trong, I. / Lybrand, T.P. / Stenkamp, R.E. / Stayton, P.S.
History
DepositionOct 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
C: PROTEIN (STREPTAVIDIN)
D: PROTEIN (STREPTAVIDIN)


Theoretical massNumber of molelcules
Total (without water)52,9494
Polymers52,9494
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-52 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.000, 66.300, 82.300
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (STREPTAVIDIN)


Mass: 13237.326 Da / Num. of mol.: 4 / Mutation: D128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria)
Description: T7 EXPRESSION SYSTEM (PET-210, NOVAGEN, INC., MADISON,WI. SYNTHETIC GENE)
Production host: Escherichia coli (E. coli) / References: UniProt: SAV_STRAV, UniProt: P22629*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 49.85 %
Crystal growpH: 4.5 / Details: 50% MPD (2-METHYL-2,4-PENTANEDIOLE), PH 4.5.
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
250 %MPD1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 13, 1996
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30500 / % possible obs: 85 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 2 / % possible all: 46
Reflection
*PLUS
Num. measured all: 56045
Reflection shell
*PLUS
% possible obs: 46 %

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWC

1swc


Resolution: 2→10 Å / Num. parameters: 14379 / Num. restraintsaints: 14409 / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3197 10 %EVERY 10TH REFLECTION
all0.191 31972 --
obs0.185 -85 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973) 201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3230 / Occupancy sum non hydrogen: 3594
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3416 0 0 178 3594
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_planes0.019
X-RAY DIFFRACTIONs_zero_chiral_vol0.107
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.056
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-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / σ(F): 4 / % reflection Rfree: 10 % / Rfactor obs: 0.167 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32 Å2

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