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- PDB-6lng: Rapid crystallization of streptavidin using charged peptides -

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Basic information

Entry
Database: PDB / ID: 6lng
TitleRapid crystallization of streptavidin using charged peptides
ComponentsStreptavidin
KeywordsPEPTIDE BINDING PROTEIN / BIOTIN-BINDING PROTEIN
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
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80000150972 Å
AuthorsMinamihata, K. / Tsukamoto, K. / Adachi, M. / Shimizu, R. / Mishina, M. / Kuroki, R. / Nagamune, T.
CitationJournal: Chem.Commun.(Camb.) / Year: 2020
Title: Genetically fused charged peptides induce rapid crystallization of proteins.
Authors: Minamihata, K. / Tsukamoto, K. / Adachi, M. / Shimizu, R. / Mishina, M. / Kuroki, R. / Nagamune, T.
History
DepositionDec 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: 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
E: Streptavidin
F: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,03912
Polymers78,4876
Non-polymers5536
Water12,827712
1
A: Streptavidin
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6938
Polymers52,3254
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint-57 kcal/mol
Surface area20260 Å2
MethodPISA
2
E: Streptavidin
F: Streptavidin
hetero molecules

E: Streptavidin
F: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6938
Polymers52,3254
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9920 Å2
ΔGint-57 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.2929992676, 80.8290023804, 132.647994995
Angle α, β, γ (deg.)90.0, 99.8460006714, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11D-390-

HOH

21E-319-

HOH

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Components

#1: Protein
Streptavidin


Mass: 13081.144 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Mixture of Two kinds of proteins, which have RRRRRRY or DDDDDDY attached at C-terminal respectively, was used in this study.
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22629
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% w/v polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→37.1 Å / Num. obs: 78148 / % possible obs: 99.7 % / Redundancy: 3.67 % / Biso Wilson estimate: 16.1760765111 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.91
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5742

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RY1

3ry1


Resolution: 1.80000150972→37.0878676876 Å / SU ML: 0.181418679282 / Cross valid method: FREE R-VALUE / σ(F): 1.3434970804 / Phase error: 22.4923699741
RfactorNum. reflection% reflection
Rfree0.218630423995 3904 4.99967983608 %
Rwork0.181202411082 74181 -
obs0.183059438376 78085 99.6210864739 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.5692769581 Å2
Refinement stepCycle: LAST / Resolution: 1.80000150972→37.0878676876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5430 0 36 712 6178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007119407695885598
X-RAY DIFFRACTIONf_angle_d1.124281213957656
X-RAY DIFFRACTIONf_chiral_restr0.0475062416558852
X-RAY DIFFRACTIONf_plane_restr0.00440049026037960
X-RAY DIFFRACTIONf_dihedral_angle_d14.73952092151890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.80000150972-1.8220.2978958416831360.2494168293362572X-RAY DIFFRACTION98.5085485631
1.822-1.8450.2544333984831400.2280283277672683X-RAY DIFFRACTION99.6118560339
1.845-1.86930.2781545521421380.2083932111272592X-RAY DIFFRACTION99.5260663507
1.8693-1.89490.25301242041390.1995337786212656X-RAY DIFFRACTION99.6079828938
1.8949-1.9220.2241768553261390.1926306767632642X-RAY DIFFRACTION99.5703544576
1.922-1.95070.2542512180881370.1892337854952606X-RAY DIFFRACTION99.7091966558
1.9507-1.98110.2174485873941410.1825647213472677X-RAY DIFFRACTION99.7169143666
1.9811-2.01360.2467432131811380.1775369555342627X-RAY DIFFRACTION99.7115037865
2.0136-2.04830.186222326641390.1731342629872644X-RAY DIFFRACTION99.6776504298
2.0483-2.08560.2162815447341390.1751832422624X-RAY DIFFRACTION99.7833152763
2.0856-2.12570.218425769521410.1688327184822694X-RAY DIFFRACTION99.6835443038
2.1257-2.16910.1941185098571370.1645298243382598X-RAY DIFFRACTION99.9634502924
2.1691-2.21620.2293291166791420.1682717220462681X-RAY DIFFRACTION99.9292035398
2.2162-2.26780.2414653197461370.1746419112172613X-RAY DIFFRACTION99.6015936255
2.2678-2.32450.235956200481410.1833549773412677X-RAY DIFFRACTION99.8936547324
2.3245-2.38730.2479360128921420.1895908767812692X-RAY DIFFRACTION99.9294781382
2.3873-2.45750.2764481241561380.188934591192623X-RAY DIFFRACTION99.8192335503
2.4575-2.53690.2163395574381370.1771321860612617X-RAY DIFFRACTION99.8911860718
2.5369-2.62750.214567863211400.182768285392658X-RAY DIFFRACTION99.8572448251
2.6275-2.73270.2206894323461420.1815789921752694X-RAY DIFFRACTION99.8591549296
2.7327-2.8570.2077359314691380.1738294525932621X-RAY DIFFRACTION99.9275624774
2.857-3.00760.2049847662111410.1809305453542678X-RAY DIFFRACTION99.7523000708
3.0076-3.19590.2022078415691400.1753654870042666X-RAY DIFFRACTION99.786628734
3.1959-3.44250.2114105779781380.1728372506032636X-RAY DIFFRACTION99.7482919813
3.4425-3.78860.1986044400931410.1740002717372676X-RAY DIFFRACTION99.5406360424
3.7886-4.33610.1971703997971400.1672575374312662X-RAY DIFFRACTION99.4675186368
4.3361-5.46030.1917104730131410.1666051509492672X-RAY DIFFRACTION99.5399858457
5.4603-37.08786768760.236214719191420.2203045352582700X-RAY DIFFRACTION97.8313253012

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