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- PDB-1swd: APO-CORE-STREPTAVIDIN IN COMPLEX WITH BIOTIN (TWO UNOCCUPIED BIND... -

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Basic information

Entry
Database: PDB / ID: 1swd
TitleAPO-CORE-STREPTAVIDIN IN COMPLEX WITH BIOTIN (TWO UNOCCUPIED BINDING SITES) 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
BIOTIN / Streptavidin
Similarity search - Component
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 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)53,6146
Polymers53,1254
Non-polymers4892
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9940 Å2
ΔGint-47 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.794, 85.191, 46.599
Angle α, β, γ (deg.)90.00, 100.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.011383, 0.94469, 0.327767), (0.943773, -0.098158, 0.315686), (0.330398, 0.312931, -0.890456)7.9741, -15.2281, 19.3527
2given(0.0087, -0.951623, -0.307145), (-0.9512, -0.102622, 0.291009), (-0.308451, 0.289624, -0.906077)14.8709, 6.6675, 27.0845
3given(-0.999677, 0.014545, -0.020849), (0.000967, -0.797791, -0.602933), (-0.025403, -0.602758, 0.79752)23.1437, 6.8045, 2.4752
4given(-0.99973, 0.009585, -0.021154), (0.00509, -0.798281, -0.602263), (-0.02266, -0.602208, 0.798017)23.1395, 6.7858, 2.2882
5given(0.00373, -0.952459, -0.304643), (-0.952256, -0.096385, 0.289687), (-0.305278, 0.289018, -0.907345)14.7181, 7.1825, 27.0605
6given(-0.001751, 0.943835, 0.330412), (0.944904, -0.106597, 0.309505), (0.327342, 0.31275, -0.891647)7.6442, -14.8446, 19.8815

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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


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growpH: 4.5
Details: PROTEIN-BIOTIN COMPLEX WAS CO-CRYSTALLIZED FROM 50% MPD (2-METHYL-PENTANE-2,4-DIOLE, PH 4.5) WITH 1.2M 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
260 %MPD1drop
31.2 Mbiotin1dropexcess
450 %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: Apr 23, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 25758 / % possible obs: 76 % / Redundancy: 7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 14
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 1.1 / % possible all: 20

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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: 1.9→10 Å / Num. parameters: 15035 / Num. restraintsaints: 14993 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.328 2550 10 %EVERY 10TH REFLECTION
all0.209 25513 --
obs0.202 -76 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3272.3 / Occupancy sum non hydrogen: 3735.2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 32 234 3755
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.026
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_vol0.094
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.095
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.018

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