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- PDB-1sld: STREPTAVIDIN, PH 7.5, BOUND TO CYCLIC DISULFIDE-BONDED PEPTIDE LI... -

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Basic information

Entry
Database: PDB / ID: 1sld
TitleSTREPTAVIDIN, PH 7.5, BOUND TO CYCLIC DISULFIDE-BONDED PEPTIDE LIGAND AC-CHPQFC-NH2
Components
  • CYCLO-AC-CHPQFC-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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: STREPTAVIDIN
P: CYCLO-AC-CHPQFC-NH2


Theoretical massNumber of molelcules
Total (without water)14,9402
Polymers14,9402
Non-polymers00
Water1,11762
1
B: STREPTAVIDIN
P: CYCLO-AC-CHPQFC-NH2

B: STREPTAVIDIN
P: CYCLO-AC-CHPQFC-NH2

B: STREPTAVIDIN
P: CYCLO-AC-CHPQFC-NH2

B: STREPTAVIDIN
P: CYCLO-AC-CHPQFC-NH2


Theoretical massNumber of molelcules
Total (without water)59,7618
Polymers59,7618
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)59.250, 59.250, 178.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsSTREPTAVIDIN IS A TETRAMERIC PROTEIN WITH I 2 2 2 MOLECULAR SYMMETRY. THE TETRAMER IS GENERATED BY THE CRYSTALLOGRAPHIC TWO-FOLD OPERATIONS IN THE I 41 2 2 SPACE GROUP.

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Components

#1: Protein STREPTAVIDIN


Mass: 14181.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Protein/peptide CYCLO-AC-CHPQFC-NH2


Mass: 758.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Density % sol: 38 %
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

DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 11347 / % possible obs: 39 % / Observed criterion σ(I): 3.5 / Redundancy: 4.7 % / Rmerge(I) obs: 0.091
Reflection
*PLUS
Highest resolution: 1.92 Å / Lowest resolution: 50 Å / Num. measured all: 52950 / Rmerge(I) obs: 0.091

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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: 2.5→7.5 Å / σ(F): 1.7
RfactorNum. reflection
Rfree0.22 -
Rwork0.194 -
obs0.194 9362
Refinement stepCycle: LAST / Resolution: 2.5→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 0 186 1420
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_d28.3
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
Highest resolution: 2 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3

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