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- PDB-1slg: STREPTAVIDIN, PH 5.6, BOUND TO PEPTIDE FCHPQNT -

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Basic information

Entry
Database: PDB / ID: 1slg
TitleSTREPTAVIDIN, PH 5.6, BOUND TO PEPTIDE FCHPQNT
Components
  • FCHPQNT
  • 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: 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: STREPTAVIDIN
M: FCHPQNT
D: STREPTAVIDIN
P: FCHPQNT


Theoretical massNumber of molelcules
Total (without water)30,0244
Polymers30,0244
Non-polymers00
Water2,864159
1
B: STREPTAVIDIN
M: FCHPQNT
D: STREPTAVIDIN
P: FCHPQNT

B: STREPTAVIDIN
M: FCHPQNT
D: STREPTAVIDIN
P: FCHPQNT


Theoretical massNumber of molelcules
Total (without water)60,0498
Polymers60,0498
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)96.240, 105.890, 48.020
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 = 148.23 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.029, -0.004), (-0.024, 0.725, 0.689), (-0.017, 0.689, -0.725)
Vector: 52.963, 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 .. M 7 D 13 .. P 7 0.845 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 FCHPQNT


Mass: 830.864 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growpH: 5.6 / Details: pH 5.6
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: 21587 / Observed criterion σ(I): 3.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Highest resolution: 1.74 Å / Lowest resolution: 50 Å / Num. measured all: 94347 / Rmerge(I) obs: 0.072

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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). THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B ...Details: CRYST1 CELL AXES CHOSEN TO CORRESPOND TO COORDINATES OF STREPTAVIDIN DEPOSITED BY WEBER ET AL. IN THE PDB (ENTRY 1PTS). THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15 AND (NOT NAME C OR NAME O) D 13, D 14, D 15 AND (NOT NAME C OR NAME O) D 46, D 47, D 48, D 49, D 50, D 51 AND (NOT NAME C OR NAME O) B 46, B 47, B 48, B 49, B 50 AND (NOT NAME C OR NAME O) B 67, B 68 AND (NOT NAME C OR NAME O) B 53 AND (NAME NE OR NAME NH1 OR NAME NH2 OR NAME CZ) B 103 AND (NAME NE OR NAME NH1 OR NAME NH2 OR NAME CZ) D 103 AND (NAME NE OR NAME NH1 OR NAME NH2 OR NAME CZ) D 84 AND (NAME NE OR NAME NH1 OR NAME NH2 OR NAME CZ) B 116 AND (NAME CG OR NAME OR NAME OE1 OR NAME OE2) M 7, P 1, P 2, B 135 M 1 WAS NOT LOCATED OR INCLUDED IN THE MODEL. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED WERE B 73, D 73, B 110, D 110, B 22, D 107, D 105. B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A TWO-FOLD RELATED B 22. THIS DISORDER CAN NOT BE PROPERLY REFINED WITH X-PLOR. SEVERAL WATERS ARE ON OR NEAR TWO-FOLD AXES, AND CAN NOT BE PROPERLY REFINED WITH X-PLOR. BULK SOLVENT WAS REFINED.
RfactorNum. reflection
Rfree0.222 -
Rwork0.187 -
obs0.187 20506
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 1.76→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2446 0 0 477 2923
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_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
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_deg27.7

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