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- PDB-5n8b: CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE AFPDYLAEYHGG -

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Basic information

Entry
Database: PDB / ID: 5n8b
TitleCRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE AFPDYLAEYHGG
Components
  • ALA-PHE-PRO-ASP-TYR-LEU-ALA-GLU-TYR-HIS-GLY-GLY-NH2
  • Streptavidin
KeywordsBIOTIN BINDING PROTEIN / STREPTAVIDIN / HPQ MOTIF / 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
Biological speciesStreptomyces avidinii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.03 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 23, 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 / pdbx_modification_feature
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
E: ALA-PHE-PRO-ASP-TYR-LEU-ALA-GLU-TYR-HIS-GLY-GLY-NH2
B: Streptavidin
C: ALA-PHE-PRO-ASP-TYR-LEU-ALA-GLU-TYR-HIS-GLY-GLY-NH2
D: Streptavidin
F: ALA-PHE-PRO-ASP-TYR-LEU-ALA-GLU-TYR-HIS-GLY-GLY-NH2
G: Streptavidin
H: ALA-PHE-PRO-ASP-TYR-LEU-ALA-GLU-TYR-HIS-GLY-GLY-NH2


Theoretical massNumber of molelcules
Total (without water)80,7528
Polymers80,7528
Non-polymers00
Water17,366964
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15990 Å2
ΔGint-87 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.319, 65.763, 78.133
Angle α, β, γ (deg.)90.00, 103.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin


Mass: 18849.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein/peptide
ALA-PHE-PRO-ASP-TYR-LEU-ALA-GLU-TYR-HIS-GLY-GLY-NH2


Mass: 1338.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 964 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M Magnesium chloride 0.1M Sodium citrate pH 5 15% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.77491 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77491 Å / Relative weight: 1
ReflectionResolution: 1.03→75.9 Å / Num. obs: 235380 / % possible obs: 99.5 % / Redundancy: 3.38 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 9.44
Reflection shellResolution: 1.03→1.12 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.65 / Num. unique obs: 54696 / CC1/2: 0.367 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSsaddata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.03→75.9 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.004 / SU ML: 0.021 / 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
Rfree0.15537 12218 4.9 %RANDOM
Rwork0.13818 ---
obs0.13904 235380 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.495 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å2-0 Å2-0.08 Å2
2---0.41 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.03→75.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 0 964 4977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024325
X-RAY DIFFRACTIONr_bond_other_d0.0020.023698
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.8985978
X-RAY DIFFRACTIONr_angle_other_deg0.88638581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0315595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55623.656186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.18115580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6441517
X-RAY DIFFRACTIONr_chiral_restr0.0870.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02989
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_it0.6580.8532200
X-RAY DIFFRACTIONr_mcbond_other0.6580.8532199
X-RAY DIFFRACTIONr_mcangle_it0.8981.282753
X-RAY DIFFRACTIONr_mcangle_other0.8981.282754
X-RAY DIFFRACTIONr_scbond_it0.7870.9712125
X-RAY DIFFRACTIONr_scbond_other0.7870.9712126
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9891.4043192
X-RAY DIFFRACTIONr_long_range_B_refined2.58512.6985266
X-RAY DIFFRACTIONr_long_range_B_other1.70110.6214968
X-RAY DIFFRACTIONr_rigid_bond_restr0.80838023
X-RAY DIFFRACTIONr_sphericity_free21.2985645
X-RAY DIFFRACTIONr_sphericity_bonded5.16358206
LS refinement shellResolution: 1.03→1.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 896 -
Rwork0.328 17288 -
obs--99.46 %
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)
10.0653-0.06690.02590.3335-0.0710.3598-0.00270.0078-0.00350.0243-0.0092-0.01130.0570.04340.01190.01970.0056-0.01090.0283-0.00150.029613.160912.540525.8257
20.1111-0.09690.10740.75840.29470.9053-0.0020.01250.02240.0338-0.0156-0.08870.00030.10330.01750.0082-0.0006-0.01870.04960.00490.045521.958421.455526.7704
30.1055-0.07610.04850.414-0.0280.4039-0.00990.00380.0082-0.0075-0.00670.0183-0.11-0.01410.01660.0340.0024-0.01550.024800.03443.30641.582315.7888
40.5734-0.0893-0.13380.36970.06680.5938-0.0228-0.00840.01410.03750.0041-0.0301-0.11280.060.01880.0384-0.0163-0.01980.03010.00070.038512.487242.125424.1282
50.0577-0.05610.01910.3854-0.07510.327-0.014-0.0079-0.00530.07470.01490.07270.0048-0.0444-0.00090.022-0.00170.00540.0297-0.00130.0414-1.118419.644233.1656
60.1176-0.1840.31281.4801-0.02061.07720.0137-0.0258-0.04790.00080.04180.18760.0006-0.1146-0.05560.01070.0006-0.00650.054-0.00030.0846-9.743218.28624.0928
70.0503-0.06090.01480.3423-0.03080.43550.01030.01210.0053-0.0816-0.0134-0.0037-0.02280.03020.00310.02570.0004-0.01050.03180.00130.03098.456930.39753.9893
80.6305-0.2737-0.04560.6471-0.11490.39360.01580.0007-0.0201-0.1276-0.00340.08710.0606-0.023-0.01240.0371-0.0022-0.03120.0295-0.00310.0406-0.794721.77833.4127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 135
2X-RAY DIFFRACTION2E1 - 13
3X-RAY DIFFRACTION3B16 - 135
4X-RAY DIFFRACTION4C1 - 13
5X-RAY DIFFRACTION5D15 - 139
6X-RAY DIFFRACTION6F1 - 13
7X-RAY DIFFRACTION7G15 - 135
8X-RAY DIFFRACTION8H1 - 13

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