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- PDB-1swe: APO-CORE-STREPTAVIDIN IN COMPLEX WITH BIOTIN AT PH 4.5 -

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Basic information

Entry
Database: PDB / ID: 1swe
TitleAPO-CORE-STREPTAVIDIN IN COMPLEX WITH BIOTIN 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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_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: STREPTAVIDIN
B: STREPTAVIDIN
C: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1038
Polymers53,1254
Non-polymers9774
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-37 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.780, 100.110, 52.010
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.688772, -0.566835, 0.451986), (-0.56632, 0.031431, -0.823586), (0.452631, -0.823231, -0.342659)12.1711, 3.624, -3.62
2given(-0.639793, 0.583962, 0.499653), (0.594748, -0.035565, 0.803125), (0.486765, 0.811002, -0.324556)25.0919, -28.0207, 15.3701
3given(0.330848, -0.016305, -0.943543), (-0.019288, -0.999759, 0.010513), (-0.943487, 0.014721, -0.331082)17.4039, -23.949, 25.712
4given(0.324213, -0.014827, -0.945868), (-0.019429, -0.999771, 0.009012), (-0.945785, 0.015456, -0.324427)17.6162, -23.9503, 25.3946
5given(-0.644095, 0.588569, 0.488598), (0.58406, -0.034083, 0.810994), (0.493979, 0.807728, -0.321807)25.4144, -27.9069, 14.942
6given(-0.68245, -0.57133, 0.455899), (-0.576994, 0.038195, -0.815855), (0.448709, -0.819831, -0.35572)12.3808, 3.7924, -3.8713

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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, COMPLEXED WITH BIOTIN / Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical
ChemComp-BTN / BIOTIN / Biotin


Mass: 244.311 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growpH: 4.5
Details: PROTEIN-BIOTIN COMPLEX WAS CO-CRYSTALLIZED FROM 50% MPD (2-METHYL-PENTANE-2,4-DIOLE, PH 4.5) WITH 2.5M EXCESS OF BIOTIN
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125-30 mg/mlprotein1drop
2100 %MPD1drop
32.5 Mbiotin1dropexcess
450 %MPD1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 13, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 24738 / % possible obs: 83 % / Redundancy: 11 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 3.4 / % possible all: 42
Reflection shell
*PLUS
% possible obs: 42 %

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Processing

Software
NameClassification
SHELXL-96model building
X-PLORmodel building
SHELXL-96refinement
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
SHELXL-96phasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWA

1swa


Resolution: 2.06→8 Å / Num. parameters: 15579 / Num. restraintsaints: 15139 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2419 10 %EVERY 10TH REFLECTION
all0.168 24460 --
obs0.161 -79 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3355 / Occupancy sum non hydrogen: 3891
Refinement stepCycle: LAST / Resolution: 2.06→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3525 0 64 302 3891
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_planes0.017
X-RAY DIFFRACTIONs_zero_chiral_vol0.104
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.017

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