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- PDB-5n8t: CRYSTAL STRUCTURE OF STREPTAVIDIN D-amino acid containing peptide... -

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Basic information

Entry
Database: PDB / ID: 5n8t
TitleCRYSTAL STRUCTURE OF STREPTAVIDIN D-amino acid containing peptide Gdlwqheatwkkq
ComponentsStreptavidin
KeywordsBiotin binding protein / STREPTAVIDIN / BIOTIN BINDING / D-AMINO ACIDS / STREPTAVIDIN 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
D-ALANINE / D-GLUTAMIC ACID / D-GLUTAMINE / D-HISTIDINE / D-LEUCINE / D-LYSINE / D-THREONINE / D-TRYPTOPHAN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsLyamichev, V. / Goodrich, L. / Sullivan, E. / Bannen, R. / Benz, J. / Albert, T. / Patel, J.
CitationJournal: Sci Rep / Year: 2017
Title: Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target.
Authors: Lyamichev, V.I. / Goodrich, L.E. / Sullivan, E.H. / Bannen, R.M. / Benz, J. / Albert, T.J. / Patel, J.J.
History
DepositionFeb 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,19310
Polymers18,8501
Non-polymers1,3439
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.779, 57.779, 84.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-326-

HOH

21A-362-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Streptavidin


Mass: 18849.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629

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Non-polymers , 9 types, 76 molecules

#2: Chemical ChemComp-DLE / D-LEUCINE


Type: D-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-DTR / D-TRYPTOPHAN


Type: D-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical ChemComp-DGN / D-GLUTAMINE


Type: D-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Chemical ChemComp-DHI / D-HISTIDINE


Type: D-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#6: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#8: Chemical ChemComp-DTH / D-THREONINE


Type: D-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#9: Chemical ChemComp-DLY / D-LYSINE


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14N2O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1M Sodium citrate pH 4.5, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.700001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.700001 Å / Relative weight: 1
ReflectionResolution: 1.61→47.72 Å / Num. obs: 18228 / % possible obs: 100 % / Redundancy: 12.48 % / CC1/2: 0.99 / Rsym value: 0.057 / Net I/σ(I): 14.94
Reflection shellResolution: 1.61→1.71 Å / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 3098 / CC1/2: 0.341 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→47.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.602 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24341 946 4.9 %RANDOM
Rwork0.20397 ---
obs0.20587 18228 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.671 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0 Å20 Å2
2---1.84 Å20 Å2
3---3.67 Å2
Refinement stepCycle: 1 / Resolution: 1.61→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 85 67 1048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021021
X-RAY DIFFRACTIONr_bond_other_d0.0020.02877
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9561402
X-RAY DIFFRACTIONr_angle_other_deg0.90832024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0515133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.02223.68438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.18215127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.595154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021171
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02237
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0722.906520
X-RAY DIFFRACTIONr_mcbond_other1.0692.906519
X-RAY DIFFRACTIONr_mcangle_it1.6924.347648
X-RAY DIFFRACTIONr_mcangle_other1.6924.348649
X-RAY DIFFRACTIONr_scbond_it1.0882.984500
X-RAY DIFFRACTIONr_scbond_other1.0852.984500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7234.433752
X-RAY DIFFRACTIONr_long_range_B_refined4.87934.0391169
X-RAY DIFFRACTIONr_long_range_B_other4.87734.0521170
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 70 -
Rwork0.415 1333 -
obs--99.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5671-0.6185-0.04992.39930.08231.4852-0.0262-0.19630.46350.18570.0292-0.1554-0.24660.0182-0.0030.11740.0262-0.01850.0418-0.03010.09244.395815.35033.0588
24.7581-2.16654.35526.5548-4.106412.418-0.0786-1.07990.41230.5627-0.04280.18160.1083-0.54320.12140.25240.0447-0.01820.3275-0.14720.0712.029612.009615.6319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 134
2X-RAY DIFFRACTION2B3 - 11

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