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- PDB-1sle: STREPTAVIDIN, PH 5.0, BOUND TO CYCLIC PEPTIDE AC-CHPQGPPC-NH2 -

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Basic information

Entry
Database: PDB / ID: 1sle
TitleSTREPTAVIDIN, PH 5.0, BOUND TO CYCLIC PEPTIDE AC-CHPQGPPC-NH2
Components
  • AC-CHPQGPPC-NH2
  • STREPTAVIDIN
KeywordsCOMPLEX(BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX(BIOTIN-BINDING PROTEIN-PEPTIDE) / COMPLEX(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
AuthorsKatz, B.A.
CitationJournal: Biochemistry / Year: 1995
Title: Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence
Authors: Katz, B.A.
History
DepositionMar 10, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: STREPTAVIDIN
M: AC-CHPQGPPC-NH2
D: STREPTAVIDIN
P: AC-CHPQGPPC-NH2


Theoretical massNumber of molelcules
Total (without water)30,0894
Polymers30,0894
Non-polymers00
Water2,342130
1
B: STREPTAVIDIN
M: AC-CHPQGPPC-NH2
D: STREPTAVIDIN
P: AC-CHPQGPPC-NH2

B: STREPTAVIDIN
M: AC-CHPQGPPC-NH2
D: STREPTAVIDIN
P: AC-CHPQGPPC-NH2


Theoretical massNumber of molelcules
Total (without water)60,1778
Polymers60,1778
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)97.650, 107.610, 49.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.029, -0.007), (-0.025, 0.724, 0.689), (-0.015, 0.689, -0.725)
Vector: 53.556, 0.628, 0.491)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 13 .. M 8 D 13 .. P 8 0.646 SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. STREPTAVIDIN IS A TETRAMERIC PROTEIN. THE CRYSTALLOGRAPHIC TRANSFORMATION GIVEN HERE GENERATES THE TETRAMER FROM THE DIMER FOUND IN THE ASYMMETRIC UNIT OF THE CRYSTALS. APPLIED TO RESIDUES: B 13 .. B 133 D 13 .. D 133 M 2 .. M 6 P 1 .. P 6 SYMMETRY1 1 1.000000 0.000000 0.000000 0.00000 SYMMETRY2 1 0.000000 -1.000000 0.000000 0.00000 SYMMETRY3 1 0.000000 0.000000 -1.000000 0.00000

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Components

#1: Protein STREPTAVIDIN


Mass: 14181.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Protein/peptide AC-CHPQGPPC-NH2


Mass: 863.018 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growpH: 5 / Details: pH 5.0
Crystal
*PLUS
Density % sol: 21 %
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
Conc.: 15 mg/ml / Common name: peptide

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 16042 / % possible obs: 56 % / Observed criterion σ(I): 3.5 / Redundancy: 4 % / Rmerge(I) obs: 0.075
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. measured all: 64474 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
SADIE/SAINT(SIEMENS)data collection
X-PLORmodel building
X-PLORrefinement
SADIEdata reduction
SAINT(SIEMENS)data reduction
X-PLORphasing
RefinementResolution: 2→7.5 Å / σ(F): 1
Details: CRYST1 CELL AXES CHOSEN TO CORRESPOND TO COORDINATES OF STREPTAVIDIN DEPOSITED BY WEBER ET AL. IN THE PDB (ENTRY 1PTS).
RfactorNum. reflection
Rfree0.233 -
Rwork0.191 -
obs0.191 14948
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 2→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 0 390 2764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.9

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