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- PDB-5n8e: CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE RDPAPAWAHGGG -

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Basic information

Entry
Database: PDB / ID: 5n8e
TitleCRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE RDPAPAWAHGGG
Components
  • ARG-ASP-PRO-ALA-PRO-ALA-TRP-ALA-HIS-GLY-GLY-GLY-NH2
  • Streptavidin
KeywordsBIOTIN BINDING PROTEIN / STREPTAVIDIN / 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
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 23, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
E: ARG-ASP-PRO-ALA-PRO-ALA-TRP-ALA-HIS-GLY-GLY-GLY-NH2
F: ARG-ASP-PRO-ALA-PRO-ALA-TRP-ALA-HIS-GLY-GLY-GLY-NH2
H: ARG-ASP-PRO-ALA-PRO-ALA-TRP-ALA-HIS-GLY-GLY-GLY-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0199
Polymers78,9737
Non-polymers462
Water11,476637
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-105 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.810, 84.733, 58.497
Angle α, β, γ (deg.)90.00, 99.40, 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 ARG-ASP-PRO-ALA-PRO-ALA-TRP-ALA-HIS-GLY-GLY-GLY-NH2


Mass: 1191.280 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2M Ammonium acetate 0.1M Sodium acetate pH 4 15% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 1.1→57.8 Å / Num. obs: 167056 / % possible obs: 96.7 % / Redundancy: 3.17 % / CC1/2: 0.999 / Rsym value: 0.031 / Net I/σ(I): 15.2
Reflection shellResolution: 1.1→1.2 Å / Num. unique obs: 37631 / CC1/2: 0.388 / Rsym value: 0.28 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→57.78 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.821 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15291 8727 5 %RANDOM
Rwork0.13462 ---
obs0.13551 167056 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.813 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å20.39 Å2
2---0.32 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.1→57.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 2 637 4473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024242
X-RAY DIFFRACTIONr_bond_other_d0.0020.023662
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.8955871
X-RAY DIFFRACTIONr_angle_other_deg0.86938498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.84923.616177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.39615581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2131519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025002
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02965
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_it0.8911.2322179
X-RAY DIFFRACTIONr_mcbond_other0.891.2322177
X-RAY DIFFRACTIONr_mcangle_it1.2071.8462743
X-RAY DIFFRACTIONr_mcangle_other1.2061.8462744
X-RAY DIFFRACTIONr_scbond_it0.9951.3482063
X-RAY DIFFRACTIONr_scbond_other0.9951.3482064
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2352.9973097
X-RAY DIFFRACTIONr_long_range_B_refined2.16915.9195054
X-RAY DIFFRACTIONr_long_range_B_other1.82515.0234888
X-RAY DIFFRACTIONr_rigid_bond_restr0.97837898
X-RAY DIFFRACTIONr_sphericity_free19.3625414
X-RAY DIFFRACTIONr_sphericity_bonded7.30657992
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 553 -
Rwork0.19 10899 -
obs--85.31 %
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)
10.00580.0042-0.01070.01970.00780.03770.0004-0.0005-0.0013-0.00070.0009-0.0017-0.0010.0021-0.00130.0133-0.0015-0.00130.0124-0.00050.00344.89742.951760.132
20.0269-0.0242-0.01020.04480.02860.0561-0.00230.0013-0.00260.0079-0.0020.00040.0113-0.00750.00430.018-0.00270.00050.0129-0.00010.0011-4.2426-12.209738.7029
30.01080.0060.00120.0173-0.01750.0547-0.00290.0020.0010.00080.0017-0.0018-0.0016-0.00140.00120.016-0.0008-0.00090.0128-0.00010.00166.9187-4.39728.9643
40.03650.0021-0.00390.0117-0.00760.011500.00060.00370.0007-0.0017-0.00010.00110.00070.00170.0149-0.0011-0.00030.0138-0.00110.00174.824615.840748.8726
50.52180.4785-0.03170.44740.04610.7246-0.01280.01480.0277-0.02020.0120.026-0.0292-0.02470.00080.02210.0016-0.00280.01130.00060.0022-6.757315.800842.8048
60.268-0.18110.22290.689-0.41050.83550.0040.01220.0058-0.0114-0.0101-0.0045-0.00560.04490.0060.0143-0.00130.00090.0163-0.00250.000817.5051-3.943634.3854
70.52150.2909-0.08030.2882-0.17690.1512-0.0037-0.0188-0.011-0.0047-0.0054-0.01010.00110.00280.00920.01590.0003-0.00140.01420.00040.001912.391-4.470656.9617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 134
2X-RAY DIFFRACTION2B15 - 136
3X-RAY DIFFRACTION3C15 - 135
4X-RAY DIFFRACTION4D16 - 135
5X-RAY DIFFRACTION5E1 - 13
6X-RAY DIFFRACTION6F2 - 13
7X-RAY DIFFRACTION7H2 - 13

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