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- PDB-6tip: Engineered streptavidin variant (YNAFM) in complex with the Strep... -

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Basic information

Entry
Database: PDB / ID: 6tip
TitleEngineered streptavidin variant (YNAFM) 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, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
AMINO GROUP / Streptavidin
Similarity search - Component
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
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 1.3Apr 7, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Jan 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
P: Strep-tag II peptide
Q: Strep-tag II peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3305
Polymers29,3144
Non-polymers161
Water93752
1
A: Streptavidin
P: Strep-tag II peptide
hetero molecules

A: Streptavidin
P: Strep-tag II peptide
hetero molecules

A: Streptavidin
P: Strep-tag II peptide
hetero molecules

A: Streptavidin
P: Strep-tag II peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,69212
Polymers58,6288
Non-polymers644
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_554y,x,-z-1/21
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area14370 Å2
ΔGint-86 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.560, 57.560, 181.929
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / 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: 0 / Auth seq-ID: 15 - 134 / Label seq-ID: 3 - 122

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

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Components

#1: Protein Streptavidin / / Coordinate model: Cα atoms only (Chain-B)


Mass: 13438.638 Da / Num. of mol.: 2
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 Strep-tag II peptide / Coordinate model: Cα atoms only (Chain-Q)


Mass: 1218.316 Da / Num. of mol.: 2 / 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: Chemical ChemComp-NH2 / AMINO GROUP / Amine


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 52.15 %
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: 1.897→91.066 Å / Num. all: 18752 / Num. obs: 18752 / % possible obs: 99.8 % / Redundancy: 9.2 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.165 / Rsym value: 0.156 / Net I/av σ(I): 1.1 / Net I/σ(I): 8 / Num. measured all: 173120
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
2.1-2.218.50.3381.72272026740.1230.3610.3384.599.9
2.21-2.3510.10.26922551225220.0860.2830.2695.7100
2.35-2.519.50.2322.32267823860.0770.2440.2326.3100
2.51-2.718.40.2012.51873822210.0730.2140.2017100
2.71-2.979.80.1553.12026020650.050.1630.1559.199.5
2.97-3.329.70.1423.21829618820.0480.150.14210.499.7
3.32-3.838.90.1283.41512117010.0450.1360.12810.6100
3.83-4.79.70.1193.71400314390.0390.1250.11911.7100
4.7-6.648.50.1253.4986411620.0460.1340.12510.899.7
6.64-57.568.50.2170.759287000.0840.2340.21710.698.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.13 Å57.56 Å
Translation4.13 Å57.56 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QBB

6qbb


Resolution: 2.1→57.63 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.162 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.165
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 937 5 %RANDOM
Rwork0.1995 ---
obs0.2009 17772 99.57 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 271.1 Å2 / Biso mean: 80.554 Å2 / Biso min: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å20 Å2
2---2.54 Å2-0 Å2
3---5.08 Å2
Refinement stepCycle: final / Resolution: 2.1→57.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 1 52 1183
Biso mean--60.95 40.07 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122048
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181756
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.6512799
X-RAY DIFFRACTIONr_angle_other_deg1.3781.5784050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2725258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.45222100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.52215281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.481510
X-RAY DIFFRACTIONr_chiral_restr0.0680.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022357
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
Refine LS restraints NCS

Ens-ID: 1 / Number: 3215 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 68 -
Rwork0.204 1289 -
all-1357 -
obs--99.71 %
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)
13.1228-0.1969-0.08723.41520.1813.44370.0676-0.0258-0.10730.16130.09960.45190.0969-0.306-0.16720.0178-0.00580.02430.04020.04130.111-15.58073.9946-42.9939
23.47260.40630.24080.1318-0.10380.255-0.13240.02120.5584-0.01630.1870.1636-0.0569-0.1042-0.05461.71340.0022-0.02551.5144-0.01140.4827-13.628.1277-2.8888
32.73251.4131-0.418211.8815-7.41574.75790.0288-0.6298-0.07330.72970.02070.0399-0.3458-0.1774-0.04950.4133-0.01320.08510.34590.11870.1687-10.8661-1.2729-29.007
410.4657-4.5845-1.87532.88142.16143.7019-0.07660.46040.69370.361-0.224-0.012-0.3516-0.36380.30060.9175-0.055-0.03710.63820.05120.4105-6.98178.7466-16.458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 135
2X-RAY DIFFRACTION2B15 - 135
3X-RAY DIFFRACTION3P3 - 10
4X-RAY DIFFRACTION4Q3 - 10

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