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- PDB-1sts: STREPTAVIDIN DIMERIZED BY DISULFIDE-BONDED PEPTIDE FCHPQNT-NH2 DIMER -

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Basic information

Entry
Database: PDB / ID: 1sts
TitleSTREPTAVIDIN DIMERIZED BY DISULFIDE-BONDED PEPTIDE FCHPQNT-NH2 DIMER
Components
  • FCHPQNT-NH2
  • STREPTAVIDIN
KeywordsCOMPLEX (GLYCOPROTEIN/PEPTIDE) / COMPLEX (GLYCOPROTEIN-PEPTIDE) / COMPLEX (GLYCOPROTEIN-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: 1.95 Å
AuthorsKatz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N.
CitationJournal: J.Biol.Chem. / Year: 1995
Title: Topochemical catalysis achieved by structure-based ligand design.
Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N.
History
DepositionSep 12, 1995Processing site: BNL
Revision 1.0Mar 8, 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
D: STREPTAVIDIN
M: FCHPQNT-NH2
P: FCHPQNT-NH2


Theoretical massNumber of molelcules
Total (without water)27,6204
Polymers27,6204
Non-polymers00
Water2,846158
1
B: STREPTAVIDIN
D: STREPTAVIDIN
M: FCHPQNT-NH2
P: FCHPQNT-NH2

B: STREPTAVIDIN
D: STREPTAVIDIN
M: FCHPQNT-NH2
P: FCHPQNT-NH2


Theoretical massNumber of molelcules
Total (without water)55,2408
Polymers55,2408
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)97.840, 105.790, 49.080
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 = 143.60 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. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 13 .. B 135 D 13 .. D 133 1.070 NONCRYSTALLOGRAPHIC TWO-FOLD RELATING PROTOMERS OF THE STREPTAVIDIN TETRAMER SYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: B 13 .. 135 APPLIED TO RESIDUES: D 13 .. 133 APPLIED TO RESIDUES: M 2 .. 7 APPLIED TO RESIDUES: P 1 .. 7 STREPTAVIDIN IS A TETRAMERIC PROTEIN. THE CRYSTALLOGRAPHIC TRANSFORMATION GIVEN HERE GENERATES THE TETRAMER FROM THE DIMER FOUND IN THE ASYMMETRIC UNIT OF THE CRYSTALS. 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: 12965.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Protein/peptide FCHPQNT-NH2


Mass: 844.937 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130-32 %satammonium sulfate1reservoir
20.1 Mpotassium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 20222 / % possible obs: 72.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
Num. measured all: 46268 / Rmerge(I) obs: 0.089

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SADIEdata reduction
SAINTdata reduction
X-PLORphasing
RefinementResolution: 1.95→7.5 Å / σ(F): 1.5
Details: CRYST1 CELL AXES CHOSEN TO CORRESPOND TO COORDINATES OF STREPTAVIDIN DEPOSITED BY WEBER ET AL. (PDB ENTRY 1PTS). SYMMETRY OPERATIONS FOR NON-STANDARD SETTING: SYMMETRY OPERATIONS ARE STANDARD.
RfactorNum. reflection% reflection
Rfree0.238 -10 %
Rwork0.191 --
obs0.191 13414 72.2 %
Refinement stepCycle: LAST / Resolution: 1.95→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 0 474 2908
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_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.525
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_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.525

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