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- PDB-6gh7: WILDTYPE CORE-STREPTAVIDIN WITH a conjugated BIOTINYLATED PYRROLIDINE -

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Basic information

Entry
Database: PDB / ID: 6gh7
TitleWILDTYPE CORE-STREPTAVIDIN WITH a conjugated BIOTINYLATED PYRROLIDINE
ComponentsStreptavidin
KeywordsBIOTIN-BINDING PROTEIN / Organocatalysis / Supramolecular chemistry / secondary amine / artificial enzyme
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-EYW / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsNodling, A.R. / Tsai, Y.H. / Luk, L.Y.P. / Rizkallah, P. / Jin, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust200730/Z/16/Z United Kingdom
Leverhulme TrustRPG-2017-195 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2018
Title: Reactivity and Selectivity of Iminium Organocatalysis Improved by a Protein Host.
Authors: Nodling, A.R. / Swiderek, K. / Castillo, R. / Hall, J.W. / Angelastro, A. / Morrill, L.C. / Jin, Y. / Tsai, Y.H. / Moliner, V. / Luk, L.Y.P.
History
DepositionMay 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
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 / _struct.title
Revision 1.2Jan 17, 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
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9008
Polymers53,6504
Non-polymers1,2504
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-56 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.631, 98.495, 52.915
Angle α, β, γ (deg.)90.00, 112.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Streptavidin /


Mass: 13412.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical
ChemComp-EYW / 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~{R})-pyrrolidin-3-yl]pentanamide


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


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25 mg/mL protein in deionised water is mixed at equal volume with 51% MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.82001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82001 Å / Relative weight: 1
ReflectionResolution: 1.08→98.49 Å / Num. obs: 198749 / % possible obs: 97.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.069 / Net I/σ(I): 6.2
Reflection shellResolution: 1.08→1.1 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.597 / Rpim(I) all: 0.446

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1mk5

1mk5


Resolution: 1.08→49.3 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.273 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18482 9761 4.9 %RANDOM
Rwork0.15902 ---
obs0.16029 188977 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.118 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0.31 Å2
2--0.05 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.08→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3567 0 84 677 4328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0143789
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183208
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.6895201
X-RAY DIFFRACTIONr_angle_other_deg1.1111.6917473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2965489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.04122.381168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97415501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8391516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02812
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_it5.4711.3061920
X-RAY DIFFRACTIONr_mcbond_other5.4591.3051919
X-RAY DIFFRACTIONr_mcangle_it4.4891.9482397
X-RAY DIFFRACTIONr_mcangle_other4.4951.952398
X-RAY DIFFRACTIONr_scbond_it2.5651.4251869
X-RAY DIFFRACTIONr_scbond_other2.5651.4261870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.992.0612797
X-RAY DIFFRACTIONr_long_range_B_refined5.18117.3614476
X-RAY DIFFRACTIONr_long_range_B_other4.67316.0244268
X-RAY DIFFRACTIONr_rigid_bond_restr5.61836997
X-RAY DIFFRACTIONr_sphericity_free26.8315421
X-RAY DIFFRACTIONr_sphericity_bonded13.67757154
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 710 -
Rwork0.298 13630 -
obs--95.22 %

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