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- PDB-5n8j: CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE D-amino acid conta... -

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Basic information

Entry
Database: PDB / ID: 5n8j
TitleCRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE D-amino acid containing peptide GyGlanvdessG
Components
  • GLY-DTY-GLY-DLE-DAL-DSG-DVA-DAS-DGL-DSN-DSN-GLY
  • Streptavidin
KeywordsSTREPTAVIDIN PEPTIDE 11101 COMPLEX / STREPTAVIDIN / BIOTIN BINDING / D-AMINO ACIDS
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
ISOPROPYL ALCOHOL / polypeptide(D) / polypeptide(D) (> 10) / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 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 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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: Streptavidin
D: Streptavidin
P: GLY-DTY-GLY-DLE-DAL-DSG-DVA-DAS-DGL-DSN-DSN-GLY
O: GLY-DTY-GLY-DLE-DAL-DSG-DVA-DAS-DGL-DSN-DSN-GLY
E: GLY-DTY-GLY-DLE-DAL-DSG-DVA-DAS-DGL-DSN-DSN-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9638
Polymers78,9037
Non-polymers601
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-68 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.665, 84.878, 57.754
Angle α, β, γ (deg.)90.00, 99.10, 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: Polypeptide(D) GLY-DTY-GLY-DLE-DAL-DSG-DVA-DAS-DGL-DSN-DSN-GLY


Mass: 1168.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium citrate pH 5.6 20% PEG4000 20% Isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.700002 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.700002 Å / Relative weight: 1
ReflectionResolution: 1.05→57.09 Å / Num. obs: 195681 / % possible obs: 99.6 % / Redundancy: 3.43 % / CC1/2: 0.999 / Rsym value: 0.036 / Net I/σ(I): 11.4
Reflection shellResolution: 1.05→1.14 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 44813 / CC1/2: 0.388 / Rsym value: 0.64 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→57.09 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.333 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19308 10211 5 %RANDOM
Rwork0.16861 ---
obs0.16982 195681 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.321 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0.26 Å2
2--0.04 Å20 Å2
3---0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.05→57.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3767 0 4 689 4460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023988
X-RAY DIFFRACTIONr_bond_other_d0.0020.023447
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9195490
X-RAY DIFFRACTIONr_angle_other_deg0.8937971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.59723.711159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.00215524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6811516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024629
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02897
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_it0.8010.862059
X-RAY DIFFRACTIONr_mcbond_other0.7990.862058
X-RAY DIFFRACTIONr_mcangle_it1.0291.2942572
X-RAY DIFFRACTIONr_mcangle_other1.0291.2942573
X-RAY DIFFRACTIONr_scbond_it0.9310.9541929
X-RAY DIFFRACTIONr_scbond_other0.9310.9541930
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0921.3852898
X-RAY DIFFRACTIONr_long_range_B_refined2.28712.2934774
X-RAY DIFFRACTIONr_long_range_B_other2.28712.2954775
X-RAY DIFFRACTIONr_rigid_bond_restr1.23637435
X-RAY DIFFRACTIONr_sphericity_free23.055471
X-RAY DIFFRACTIONr_sphericity_bonded5.14857547
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 773 -
Rwork0.335 14341 -
obs--99.63 %
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)
10.3814-0.125-0.11560.4968-0.33710.7594-0.0402-0.1369-0.03030.05130.08920.04730.0222-0.0629-0.0490.05610.00840.01320.08290.01630.00966.678611.308128.4582
20.5087-0.0879-0.08030.3965-0.27111.01370.01380.09910.005-0.09550.02060.00820.066-0.0584-0.03440.0626-0.00880.0090.05260.00180.00438.426918.7433-2.0049
30.4158-0.1258-0.00280.5313-0.40850.9571-0.0273-0.0707-0.0716-0.09130.0095-0.02930.21640.07620.01770.0940.01840.01750.04870.00810.020217.31933.202618.844
40.4872-0.0849-0.060.4025-0.22480.93560.0191-0.00840.11560.03170.0241-0.0084-0.1869-0.029-0.04330.08040.0030.0220.0332-0.00140.03178.96531.04959.1443
51.5098-0.6046-0.66280.7310.93442.2844-0.0154-0.08080.10380.02240.0326-0.0653-0.21830.1992-0.01720.0916-0.03360.00790.0612-0.0110.037119.984331.647414.1702
60.4462-1.0211-0.24232.9577-0.11910.8672-0.02250.0081-0.0456-0.02520.10770.19770.0817-0.1658-0.08520.0509-0.00340.01190.14060.04180.0314-3.610911.001923.3151
70.65-1.10730.05571.92950.15562.61430.06750.0275-0.0579-0.1079-0.01430.10660.1551-0.2229-0.05320.0822-0.0601-0.01560.14730.03520.0156-1.044112.0990.1947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 135
2X-RAY DIFFRACTION2B15 - 134
3X-RAY DIFFRACTION3C15 - 134
4X-RAY DIFFRACTION4D15 - 134
5X-RAY DIFFRACTION5P1 - 9
6X-RAY DIFFRACTION6O4 - 10
7X-RAY DIFFRACTION7E3 - 10

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