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- PDB-5n8w: CRYSTAL STRUCTURE OF STREPTAVIDIN with D-amino acid containing pe... -

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Basic information

Entry
Database: PDB / ID: 5n8w
TitleCRYSTAL STRUCTURE OF STREPTAVIDIN with D-amino acid containing peptide GGwhdeatwkpG
Components
  • GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY
  • Streptavidin
Keywordsbiotin binding protein / STREPTAVIDIN / BIOTIN BINDING / D-AMINO ACIDS / STREPTAVIDIN PEPTIDE COMPLEX / STREPTAVIDIN PEPTIDE 11101 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
polypeptide(D) / polypeptide(D) (> 10) / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 20, 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

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
C: GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY
D: GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY


Theoretical massNumber of molelcules
Total (without water)40,9354
Polymers40,9354
Non-polymers00
Water7,440413
1
A: Streptavidin
B: Streptavidin
C: GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY
D: GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY

A: Streptavidin
B: Streptavidin
C: GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY
D: GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY


Theoretical massNumber of molelcules
Total (without water)81,8708
Polymers81,8708
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area13370 Å2
ΔGint-89 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.882, 95.720, 82.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Streptavidin


Mass: 18849.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Polypeptide(D) GLY-GLY-DTR-DHI-DAS-DGL-DAL-DTH-DTR-DLY


Mass: 1617.739 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
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: 34.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Magnesium acetate 0.1M MOPS pH 7.5 12% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.1→62.3 Å / Num. obs: 122566 / % possible obs: 99.2 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.4
Reflection shellResolution: 1.1→1.2 Å / Redundancy: 5.29 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.01 / Num. unique obs: 28666 / CC1/2: 0.792 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→62.3 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.639 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15093 6448 5 %RANDOM
Rwork0.13521 ---
obs0.13599 122566 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0 Å2
2--0.07 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.1→62.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 0 413 2399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022151
X-RAY DIFFRACTIONr_bond_other_d0.0020.021848
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9562963
X-RAY DIFFRACTIONr_angle_other_deg0.84934294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2395291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.82523.73583
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.04715283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.931159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02495
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_it0.4840.6581084
X-RAY DIFFRACTIONr_mcbond_other0.4810.6571083
X-RAY DIFFRACTIONr_mcangle_it0.6870.9861356
X-RAY DIFFRACTIONr_mcangle_other0.6870.9871357
X-RAY DIFFRACTIONr_scbond_it0.4990.7221067
X-RAY DIFFRACTIONr_scbond_other0.4990.7221068
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6041.0461592
X-RAY DIFFRACTIONr_long_range_B_refined2.0339.5792556
X-RAY DIFFRACTIONr_long_range_B_other2.0329.5762556
X-RAY DIFFRACTIONr_rigid_bond_restr1.05733999
X-RAY DIFFRACTIONr_sphericity_free17.3155287
X-RAY DIFFRACTIONr_sphericity_bonded3.64354063
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 476 -
Rwork0.331 8513 -
obs--94.23 %
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)
10.42650.024-0.0260.47680.0480.68410.0098-0.05050.02280.0652-0.01560.0282-0.0073-0.03310.00580.0194-0.00180.00410.00880.00030.024627.614226.812429.6079
20.40550.05780.05520.48170.04180.66570.00250.0442-0.0149-0.0676-0.00920.03820.0262-0.03710.00670.0211-0.0006-0.00750.00880.00060.025926.488221.03213.4816
32.00940.7658-0.49331.9007-0.91882.179-0.04840.0799-0.2022-0.0872-0.0136-0.07230.24280.01390.0620.0566-0.00040.00140.0051-0.01170.054530.35878.303313.9723
41.1295-0.37150.30862.6195-1.0891.6304-0.019-0.03960.16490.0662-0.033-0.0364-0.18710.00980.05210.0485-0-0.00160.0024-0.00790.055631.059240.643927.9546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 136
2X-RAY DIFFRACTION2B15 - 135
3X-RAY DIFFRACTION3C1 - 10
4X-RAY DIFFRACTION4D1 - 12

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