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- PDB-1slf: APOSTREPTAVIDIN, PH 5.6, TWO MOLECULES OF (SO4)2 BOUND AT THE BIO... -

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Basic information

Entry
Database: PDB / ID: 1slf
TitleAPOSTREPTAVIDIN, PH 5.6, TWO MOLECULES OF (SO4)2 BOUND AT THE BIOTIN BINDING SITE
ComponentsSTREPTAVIDIN
KeywordsBIOTIN-BINDING PROTEIN
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: 1.76 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 1.3Feb 14, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7476
Polymers28,3632
Non-polymers3844
Water3,243180
1
B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules

B: STREPTAVIDIN
D: STREPTAVIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,49412
Polymers56,7254
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)95.430, 106.120, 47.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: LYS B 134 - PRO B 135 OMEGA = 147.06 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.027, -0.003), (-0.022, 0.725, 0.689), (-0.016, 0.688, -0.725)
Vector: 52.275, 0.539, 0.403)
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. NONCRYSTALLOGRAPHIC TWO-FOLD RELATING PROTOMERS OF THE STREPTAVIDIN TETRAMER APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 13 .. B 133 D 13 .. D 133 0.731 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 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130-32 mg/mlammonium sulfate1reservoir
20.1 Mpotassium acetate1reservoir
330 mg/mlprotein1drop

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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: 22185 / Observed criterion σ(I): 3.5 / Redundancy: 4.2 % / Rmerge(I) obs: 0.073
Reflection
*PLUS
Highest resolution: 1.74 Å / Lowest resolution: 50 Å / Num. measured all: 93159 / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
SADIEdata reduction
SAINT(SIEMENS)data reduction
X-PLORphasing
RefinementResolution: 1.76→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
Rfree0.202 -
Rwork0.176 -
obs0.176 21115
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 1.76→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 20 540 2861
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_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
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: 1.74 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_deg27.8
LS refinement shell
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 1.84 Å

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