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- PDB-1pts: CRYSTAL STRUCTURE AND LIGAND BINDING STUDIES OF A SCREENED PEPTID... -

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Basic information

Entry
Database: PDB / ID: 1pts
TitleCRYSTAL STRUCTURE AND LIGAND BINDING STUDIES OF A SCREENED PEPTIDE COMPLEXED WITH STREPTAVIDIN
Components
  • PEPTIDE (FSHPQNT)
  • STREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN/PEPTIDE / GLYCOPROTEIN / BIOTIN-BINDING PROTEIN-PEPTIDE complex
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 / Resolution: 2 Å
AuthorsWeber, P.C. / Pantoliano, M.W. / Thompson, L.D.
Citation
Journal: Biochemistry / Year: 1992
Title: Crystal structure and ligand-binding studies of a screened peptide complexed with streptavidin.
Authors: Weber, P.C. / Pantoliano, M.W. / Thompson, L.D.
#1: Journal: J.Am.Chem.Soc. / Year: 1992
Title: Crystallographic and Thermodynamic Comparison of Natural and Synthetic Ligands Bound to Streptavidin
Authors: Weber, P.C. / Wendoloski, J.J. / Pantoliano, M.W. / Salemme, F.R.
#2: Journal: Science / Year: 1989
Title: Structural Origins of High-Affinity Biotin Binding to Streptavidin
Authors: Weber, P.C. / Ohlendorf, D.H. / Wendoloski, J.J. / Salemme, F.R.
History
DepositionJul 23, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jan 24, 2018Group: Other / Structure summary / Category: audit_author / pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STREPTAVIDIN
B: STREPTAVIDIN
P: PEPTIDE (FSHPQNT)


Theoretical massNumber of molelcules
Total (without water)26,3083
Polymers26,3083
Non-polymers00
Water4,342241
1
A: STREPTAVIDIN
B: STREPTAVIDIN
P: PEPTIDE (FSHPQNT)

A: STREPTAVIDIN
B: STREPTAVIDIN
P: PEPTIDE (FSHPQNT)


Theoretical massNumber of molelcules
Total (without water)52,6176
Polymers52,6176
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
A: STREPTAVIDIN
B: STREPTAVIDIN
P: PEPTIDE (FSHPQNT)

A: STREPTAVIDIN
B: STREPTAVIDIN
P: PEPTIDE (FSHPQNT)

A: STREPTAVIDIN
B: STREPTAVIDIN
P: PEPTIDE (FSHPQNT)

A: STREPTAVIDIN
B: STREPTAVIDIN
P: PEPTIDE (FSHPQNT)


Theoretical massNumber of molelcules
Total (without water)105,23312
Polymers105,23312
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)95.200, 106.500, 47.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein STREPTAVIDIN


Mass: 12738.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Protein/peptide PEPTIDE (FSHPQNT) / Coordinate model: Cα atoms only


Mass: 830.864 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 15804 / Rmerge(I) obs: 0.069

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Processing

Software
NameClassification
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.179 / Rfactor obs: 0.179 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 0 241 1974
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 15592 / Rfactor obs: 0.179 / Rfactor Rwork: 0.179
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 0.039

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