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- PDB-6qbb: Engineered streptavidin variant (ENAGY) in complex with the Strep... -

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Basic information

Entry
Database: PDB / ID: 6qbb
TitleEngineered streptavidin variant (ENAGY) 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 / Resolution: 1.52 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
DepositionDec 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Refinement description
Category: citation / citation_author / pdbx_refine_tls_group
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.2Jan 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
P: Strep-tag II peptide
B: Streptavidin
Q: Strep-tag II peptide


Theoretical massNumber of molelcules
Total (without water)29,8414
Polymers29,8414
Non-polymers00
Water4,107228
1
A: Streptavidin
P: Strep-tag II peptide
B: Streptavidin
Q: Strep-tag II peptide

A: Streptavidin
P: Strep-tag II peptide
B: Streptavidin
Q: Strep-tag II peptide


Theoretical massNumber of molelcules
Total (without water)59,6828
Polymers59,6828
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area13660 Å2
ΔGint-67 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.560, 64.170, 78.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 15 - 132 / Label seq-ID: 3 - 120

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BC

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Components

#1: Protein Streptavidin


Mass: 13346.434 Da / Num. of mol.: 2
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: 1574.123 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide SAWSHPQFEK carries an anthraniloyl/2-aminobenzoyl (Abz) 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.: 228 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG MME 550, zinc sulfate, 2-(N-morpholino)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: 1.52→49.58 Å / Num. obs: 35992 / % possible obs: 100 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.039 / Rrim(I) all: 0.085 / Net I/σ(I): 11.1
Reflection shellResolution: 1.52→1.6 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.342 / Num. unique obs: 5162 / Rpim(I) all: 0.176 / Rrim(I) all: 0.386 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RST

1rst


Resolution: 1.52→49.58 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.721 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19021 1768 4.9 %RANDOM
Rwork0.16154 ---
obs0.16295 34172 99.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 18.109 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å2-0 Å20 Å2
2--1.99 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: 1 / Resolution: 1.52→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 0 228 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022012
X-RAY DIFFRACTIONr_bond_other_d0.0040.021770
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.8922757
X-RAY DIFFRACTIONr_angle_other_deg1.06734047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.7323.48389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2515271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2281510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022375
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02519
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_it2.3471.2651030
X-RAY DIFFRACTIONr_mcbond_other2.3491.2641028
X-RAY DIFFRACTIONr_mcangle_it3.6291.8761284
X-RAY DIFFRACTIONr_mcangle_other3.6291.8751284
X-RAY DIFFRACTIONr_scbond_it2.7731.562982
X-RAY DIFFRACTIONr_scbond_other2.7711.562983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0022.2491470
X-RAY DIFFRACTIONr_long_range_B_refined6.49912.6512461
X-RAY DIFFRACTIONr_long_range_B_other6.42612.1322366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5699 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 133 -
Rwork0.212 2473 -
obs--99.43 %
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)
10.39710.0214-0.02590.26880.00650.1249-0.0178-0.0849-0.0243-0.00020.02560.0010.00590.0193-0.00780.0237-0.00320.00630.0544-0.00090.004-3.4564-28.076915.5502
23.1401-2.0087-0.2591.6149-0.28990.65120.1106-0.00180.0582-0.1233-0.0623-0.01290.05990.0748-0.04830.03610.0078-0.0260.03570.00480.030210.1799-32.429511.1319
30.0639-0.0638-0.10480.11320.04980.28010.00940.01190.0071-0.0152-0.00610.0093-0.0203-0.0103-0.00330.0278-0.00840.0040.03170.00250.0277-9.2941-16.93974.2938
41.6992-0.45151.02022.2236-1.32511.14160.1167-0.0582-0.0829-0.1490.02410.17930.131-0.0543-0.14080.03160.0314-0.01450.08980.00530.0158-22.6895-20.8148-0.3732
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 135
2X-RAY DIFFRACTION2P3 - 10
3X-RAY DIFFRACTION2P11
4X-RAY DIFFRACTION3B15 - 133
5X-RAY DIFFRACTION4Q3 - 10
6X-RAY DIFFRACTION4Q11

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