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- PDB-6qw4: Engineered streptavidin variant (ACGR) in complex with the Strep-... -

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Basic information

Entry
Database: PDB / ID: 6qw4
TitleEngineered streptavidin variant (ACGR) in complex with the Strep-tag II peptide
Components
  • Strep-tag II peptide
  • Streptavidin
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 / 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 / molecular replacement / Resolution: 2.1 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
DepositionMar 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.title
Revision 2.0May 12, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / 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_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _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_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_ref_seq_dif.details
Revision 2.1Jan 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
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
P: Strep-tag II peptide


Theoretical massNumber of molelcules
Total (without water)14,6952
Polymers14,6952
Non-polymers00
Water1,02757
1
A: Streptavidin
P: Strep-tag II peptide

A: Streptavidin
P: Strep-tag II peptide

A: Streptavidin
P: Strep-tag II peptide

A: Streptavidin
P: Strep-tag II peptide


Theoretical massNumber of molelcules
Total (without water)58,7808
Polymers58,7808
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area13410 Å2
ΔGint-66 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.160, 57.160, 175.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

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Components

#1: Protein Streptavidin


Mass: 13359.586 Da / Num. of mol.: 1
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 Strep-tag II peptide


Mass: 1335.445 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide SAWSHPQFEK 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.: 57 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: lithium sulfate, 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2013 / Details: Si mirror
RadiationMonochromator: Si 111 Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→54.337 Å / Num. obs: 8934 / % possible obs: 100 % / Redundancy: 10 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.123 / Rsym value: 0.117 / Net I/av σ(I): 4.8 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.1-2.2110.30.36212610.1170.3790.36100
2.21-2.35100.3431.612000.1180.3630.343100
2.35-2.5110.20.2353.111440.0770.2480.235100
2.51-2.7110.10.183.810570.0590.1890.18100
2.71-2.9710.20.1036.99850.0340.1090.103100
2.97-3.3210.10.071108980.0230.0740.071100
3.32-3.839.90.0877.18080.0290.0910.087100
3.83-4.79.80.0857.26830.0280.090.085100
4.7-6.649.50.0529.85540.0170.0550.052100
6.64-36.6968.30.03513.83440.0120.0370.03599.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å36.7 Å
Translation2.1 Å36.7 Å

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Processing

Software
NameVersionClassification
MOSFLM7.0.9data reduction
SCALA3.3.20data scaling
PHASER2.5.6phasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RST

1rst


Resolution: 2.1→36.72 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.795 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.178
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 423 4.7 %RANDOM
Rwork0.2 ---
obs0.2018 8486 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 57.76 Å2 / Biso mean: 20.896 Å2 / Biso min: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å2-0 Å2
2--0.19 Å2-0 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 2.1→36.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 1 57 1021
Biso mean--43.39 27.05 -
Num. residues----128
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.014995
X-RAY DIFFRACTIONr_bond_other_d0.0010.018837
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.6631361
X-RAY DIFFRACTIONr_angle_other_deg1.0651.6551949
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8755128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.45621.91547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12415136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.702155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02210
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 35 -
Rwork0.145 592 -
all-627 -
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)
10.4326-0.4153-0.04410.5661-0.18670.32140.0296-0.03460.067-0.07970.0191-0.03570.06990.0297-0.04860.02070.0089-0.0060.0197-0.01210.016515.2163.986-2.896
23.26011.04030.45816.0370.72150.12320.04460.4475-0.61-0.42210.0678-0.2564-0.03910.0528-0.11240.0660.01880.0210.0899-0.06670.144313.322-0.588-15.079
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 135
2X-RAY DIFFRACTION2P4 - 10
3X-RAY DIFFRACTION2P101

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