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- PDB-6zyt: Monomeric streptavidin with a conjugated biotinylated pyrrolidine -

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Basic information

Entry
Database: PDB / ID: 6zyt
TitleMonomeric streptavidin with a conjugated biotinylated pyrrolidine
ComponentsStreptavidin/Rhizavidin Hybrid
KeywordsDE NOVO PROTEIN / Biotin-binding protein / streptavidin / artificial enzyme / beta-barrel
Function / homologyChem-UJE
Function and homology information
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNodling, A.R. / Lipka-Lloyd, M. / Tsai, Y.H. / Rizkallah, P. / Luk, L.Y.P. / Jin, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-195 United Kingdom
Wellcome Trust202056/Z/16/Z United Kingdom
Citation
Journal: Org.Biomol.Chem. / Year: 2021
Title: The role of streptavidin and its variants in catalysis by biotinylated secondary amines.
Authors: Nodling, A.R. / Santi, N. / Castillo, R. / Lipka-Lloyd, M. / Jin, Y. / Morrill, L.C. / Swiderek, K. / Moliner, V. / Luk, L.Y.P.
#1: Journal: Biotechnol. Bioeng. / Year: 2013
Title: Stable, high-affinity streptavidin monomer for protein labeling and monovalent biotin detection.
Authors: Lim, K.H. / Huang, H. / Pralle, A. / Park, S.
History
DepositionAug 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BBB: Streptavidin/Rhizavidin Hybrid
AAA: Streptavidin/Rhizavidin Hybrid
CCC: Streptavidin/Rhizavidin Hybrid
FFF: Streptavidin/Rhizavidin Hybrid
DDD: Streptavidin/Rhizavidin Hybrid
EEE: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,45315
Polymers95,2906
Non-polymers2,1639
Water4,504250
1
BBB: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3864
Polymers15,8821
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
AAA: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2903
Polymers15,8821
Non-polymers4082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1942
Polymers15,8821
Non-polymers3121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
FFF: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1942
Polymers15,8821
Non-polymers3121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
DDD: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1942
Polymers15,8821
Non-polymers3121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
EEE: Streptavidin/Rhizavidin Hybrid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1942
Polymers15,8821
Non-polymers3121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.790, 52.740, 89.360
Angle α, β, γ (deg.)75.240, 78.240, 84.880
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Streptavidin/Rhizavidin Hybrid


Mass: 15881.708 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UJE / 5-((3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)-N-((S)-pyrrolidin-3-yl)pentanamide / 5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[(3~{S})-pyrrolidin-3-yl]pentanamide


Mass: 312.431 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H24N4O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.32 % / Description: large plates
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.8→25.48 Å / Num. obs: 64049 / % possible obs: 95.7 % / Redundancy: 1.7 % / CC1/2: 0.967 / Net I/σ(I): 5.6
Reflection shellResolution: 1.8→1.84 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3764 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jnj

4jnj


Resolution: 1.8→25.48 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.206 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.184 / ESU R Free: 0.17
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3008 3144 4.909 %
Rwork0.2585 60905 -
all0.261 --
obs-64049 95.687 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.459 Å20.254 Å2-0.194 Å2
2---2.301 Å2-0.65 Å2
3---2.038 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 141 250 5587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135516
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184469
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6997507
X-RAY DIFFRACTIONr_angle_other_deg1.2681.62610433
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.825670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07722.955335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89215788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7241538
X-RAY DIFFRACTIONr_chiral_restr0.0680.2709
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021280
X-RAY DIFFRACTIONr_nbd_refined0.1740.2848
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24112
X-RAY DIFFRACTIONr_nbtor_refined0.1620.22385
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.22558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.221
X-RAY DIFFRACTIONr_nbd_other0.1830.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2210.210
X-RAY DIFFRACTIONr_mcbond_it1.9913.7252686
X-RAY DIFFRACTIONr_mcbond_other1.9913.7242685
X-RAY DIFFRACTIONr_mcangle_it3.0285.5743354
X-RAY DIFFRACTIONr_mcangle_other3.0275.5753355
X-RAY DIFFRACTIONr_scbond_it2.1173.8052830
X-RAY DIFFRACTIONr_scbond_other2.1173.8052831
X-RAY DIFFRACTIONr_scangle_it3.2635.6344153
X-RAY DIFFRACTIONr_scangle_other3.2635.6344154
X-RAY DIFFRACTIONr_lrange_it5.24440.5655886
X-RAY DIFFRACTIONr_lrange_other5.24340.5645887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3412390.3084436X-RAY DIFFRACTION94.9046
1.847-1.8970.3522090.3124439X-RAY DIFFRACTION94.7798
1.897-1.9520.361940.3644140X-RAY DIFFRACTION93.5867
1.952-2.0120.3392110.2984144X-RAY DIFFRACTION94.7976
2.012-2.0780.3141980.2713936X-RAY DIFFRACTION94.3405
2.078-2.1510.3161910.2693847X-RAY DIFFRACTION94.9001
2.151-2.2320.3771780.2663731X-RAY DIFFRACTION94.4659
2.232-2.3230.3351920.2943596X-RAY DIFFRACTION95.0326
2.323-2.4270.3371500.2383506X-RAY DIFFRACTION96.3373
2.427-2.5450.3261700.2663328X-RAY DIFFRACTION96.3902
2.545-2.6820.3531820.2573136X-RAY DIFFRACTION96.5658
2.682-2.8450.291510.263007X-RAY DIFFRACTION96.6636
2.845-3.0410.3341430.2572874X-RAY DIFFRACTION97.354
3.041-3.2850.2871480.262634X-RAY DIFFRACTION97.5456
3.285-3.5970.2991570.2512396X-RAY DIFFRACTION97.2201
3.597-4.0210.2321230.2262213X-RAY DIFFRACTION97.9866
4.021-4.6420.2451240.2181922X-RAY DIFFRACTION97.1049
4.642-5.680.277990.2411626X-RAY DIFFRACTION97.5679
5.68-8.0150.356530.2871300X-RAY DIFFRACTION98.4

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