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- PDB-6sos: Engineered streptavidin variant (ENAGY) in complex with the Twin-... -

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Basic information

Entry
Database: PDB / ID: 6sos
TitleEngineered streptavidin variant (ENAGY) in complex with the Twin-Strep-tag peptide
Components
  • Streptavidin
  • Twin-Strep-tag peptide
KeywordsPEPTIDE BINDING PROTEIN / LOOP ENGINEERING / PROTEIN ENGINEERING / STREP-TAG / STREPTAVIDIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like, conserved site / Avidin-like domain signature. / Avidin / : / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSkerra, A. / Eichinger, A.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: The Role of Changing Loop Conformations in Streptavidin Versions Engineered for High-affinity Binding of the Strep-tag II Peptide.
Authors: Schmidt, T.G.M. / Eichinger, A. / Schneider, M. / Bonet, L. / Carl, U. / Karthaus, D. / Theobald, I. / Skerra, A.
History
DepositionAug 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 17, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref_seq / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_site_gen.label_asym_id
Revision 2.1Apr 7, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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
P: Twin-Strep-tag peptide
R: Twin-Strep-tag peptide


Theoretical massNumber of molelcules
Total (without water)59,7186
Polymers59,7186
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13580 Å2
ΔGint-73 kcal/mol
Surface area20310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.769, 101.769, 118.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALYSLYSAA15 - 1343 - 122
21ALAALALYSLYSBB15 - 1343 - 122
12ALAALAVALVALAA15 - 1333 - 121
22ALAALAVALVALCC15 - 1333 - 121
13ALAALAVALVALAA15 - 1333 - 121
23ALAALAVALVALDD15 - 1333 - 121
14GLUGLUVALVALBB14 - 1332 - 121
24GLUGLUVALVALCC14 - 1332 - 121
15GLUGLUVALVALBB14 - 1332 - 121
25GLUGLUVALVALDD14 - 1332 - 121
16GLUGLULYSLYSCC14 - 1342 - 122
26GLUGLULYSLYSDD14 - 1342 - 122

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Streptavidin


Mass: 13346.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: engineered protein / Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Protein/peptide Twin-Strep-tag peptide


Mass: 3166.316 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide SAWSHPQFEKGGGSGGGSGGSAWSHPQFEK carries an anthraniloyl/2-aminobenzoyl (BE2) group at the N-terminus and an amide group at the C-terminus.
Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2015 / Details: Si mirror
RadiationMonochromator: Si 111 Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91801 Å / Relative weight: 1
ReflectionResolution: 2.2→77.25 Å / Num. obs: 32346 / % possible obs: 100 % / Redundancy: 11.2 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.102 / Rsym value: 0.098 / Net I/av σ(I): 6.3 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3211.80.3222.35454046330.0980.3370.3226.9100
2.32-2.4611.50.2782.75034243790.0850.2910.2787.7100
2.46-2.6310.50.2223.34334441400.0720.2340.2229.2100
2.63-2.84110.1634.54285038780.0510.1710.16312.9100
2.84-3.1111.70.1245.74169435640.0380.130.12417.4100
3.11-3.4810.70.0927.33469032520.0290.0970.09223100
3.48-4.0211.60.06410.43368528920.0190.0670.06430.4100
4.02-4.92110.0649.92712924740.020.0670.06433100
4.92-6.9610.90.059102130019630.0190.0620.05928.3100
6.96-77.2499.80.04610.21151111710.0160.0490.04626.599.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.01 Å46.78 Å
Translation6.01 Å46.78 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.1data reduction
SCALA3.3.22data scaling
PHASER2.5.6phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QBB

6qbb


Resolution: 2.2→77.25 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.781 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2496 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.2
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1586 4.9 %RANDOM
Rwork0.212 ---
obs0.2137 30694 99.96 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 149.93 Å2 / Biso mean: 27.953 Å2 / Biso min: 11.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---0.96 Å20 Å2
3---1.92 Å2
Refinement stepCycle: final / Resolution: 2.2→77.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3902 0 2 129 4033
Biso mean--50.73 28.03 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124000
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183419
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.6515460
X-RAY DIFFRACTIONr_angle_other_deg1.3041.5777890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2895510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.64522.194196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09215544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9321520
X-RAY DIFFRACTIONr_chiral_restr0.0620.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35710.08
12B35710.08
21A35140.08
22C35140.08
31A35700.07
32D35700.07
41B35880.07
42C35880.07
51B36290.05
52D36290.05
61C36170.07
62D36170.07
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 115 -
Rwork0.181 2233 -
all-2348 -
obs--100 %
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)
10.73390.1484-0.09060.06990.00750.0419-0.0248-0.02950.03330.0265-0.00510.0581-0.00630.01530.02990.1073-0.01090.02670.0663-0.00190.072515.82423.827-22.647
20.05780.0627-0.11070.434-0.08680.2938-0.02520.0232-0.02620.00320.0110.00770.0270.0360.01420.0765-0.02470.00710.1187-0.02480.07423.644414.3447-35.0095
30.52880.2857-0.05330.1596-0.02480.01390.0343-0.06540.0360.0336-0.01920.019-0.00370.0278-0.01520.1033-0.0009-0.00850.0905-0.00050.054939.86538.9631-22.1715
40.1320.05350.01190.27250.15050.21460.00240.06670-0.0230.01220.02390.00010.0355-0.01450.0859-0.0002-0.00370.10610.02020.052639.957537.2155-39.1331
50.58680.897-0.34732.14130.4091.358-0.0221-0.0773-0.1886-0.0127-0.0722-0.28750.01750.09110.09440.03990.0556-0.0050.09720.04080.130539.883518.1255-23.1597
64.07971.0181-2.14381.2552-1.63072.4744-0.02010.05150.1053-0.0501-0.03050.08890.01290.04080.05060.0769-0.0163-0.04510.00740.01410.205420.109138.5139-36.2815
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 136
2X-RAY DIFFRACTION2B14 - 135
3X-RAY DIFFRACTION3C14 - 134
4X-RAY DIFFRACTION4D14 - 134
5X-RAY DIFFRACTION5P4 - 31
6X-RAY DIFFRACTION6R4 - 31

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