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- PDB-7alx: Sav-SOD: Chimeric Streptavidin-cSOD as Host for Artificial Metall... -

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Basic information

Entry
Database: PDB / ID: 7alx
TitleSav-SOD: Chimeric Streptavidin-cSOD as Host for Artificial Metalloenzymes
ComponentsStreptavidin,Superoxide dismutase [Cu-Zn],Streptavidin
KeywordsMETAL BINDING PROTEIN / biotin-binding protein
Function / homology
Function and homology information


biotin binding / superoxide dismutase / superoxide dismutase activity / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / : / Avidin-like, conserved site / Avidin-like domain signature. / Avidin ...Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Superoxide dismutase-like, copper/zinc binding domain superfamily / : / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-UFW / Superoxide dismutase [Cu-Zn] / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
Mycobacterium bovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIgareta, N.V. / Christoffel, F. / Peterson, R.L. / Ward, T.R.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation200020_182046 Switzerland
European Research Council (ERC)694424 Switzerland
CitationJournal: Nat Catal / Year: 2021
Title: Design and evolution of chimeric streptavidin for protein-enabled dual gold catalysis
Authors: Christoffel, F. / Igareta, N.V. / Pellizzoni, M.M. / Tiessler-Sala, L. / Lozhkin, B. / Spiess, D.C. / Lledos, A. / Marechal, J.D. / Peterson, R.L. / Ward, T.R.
History
DepositionOct 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 17, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / database_2 / pdbx_database_proc
Item: _atom_site.calc_flag / _citation.country ..._atom_site.calc_flag / _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.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin
BBB: Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6574
Polymers40,1392
Non-polymers1,5172
Water2,810156
1
AAA: Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin
BBB: Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin
hetero molecules

AAA: Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin
BBB: Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3148
Polymers80,2794
Non-polymers3,0354
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
Buried area9030 Å2
ΔGint-57 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.525, 102.525, 59.077
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11AAA-323-

HOH

21BBB-318-

HOH

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Components

#1: Protein Streptavidin,Superoxide dismutase [Cu-Zn],Streptavidin


Mass: 20069.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria), (gene. exp.) Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97) (bacteria)
Strain: ATCC BAA-935 / AF2122/97 / Gene: sodC, BQ2027_MB0440 / Production host: Escherichia coli (E. coli)
References: UniProt: P22629, UniProt: P0A609, superoxide dismutase
#2: Chemical ChemComp-UFW / ((4S)-1,3-dimesityl-4-((5-((3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamido)methyl)imidazolidin-2-yl)gold / [(4~{S})-4-[[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]pentanoylamino]methyl]-1,3-bis(2,4,6-trimethylphenyl)imidazolidin-2-ylidene]gold / [(4S)-4-[[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]methyl]-1,3-bis(2,4,6-trimethylphenyl)imidazolidin-2-ylidene]gold


Mass: 758.748 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H43AuN5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 %w/v PEG 3350 (Precipitant) 0.2 M Na K Phos (Salt) 0.1 M BIS-TRIS prop 7.5 pH (Buffer)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.8→45.893 Å / Num. obs: 29784 / % possible obs: 100 % / Redundancy: 24.4 % / CC1/2: 0.999 / Net I/σ(I): 18.9
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 1719 / CC1/2: 0.958 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
PHASERphasing
Aimless0.7.4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IRW

4irw


Resolution: 1.8→45.893 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.197 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2182 1445 4.858 %
Rwork0.1794 28298 -
all0.181 --
obs-29743 99.97 %
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: 27.668 Å2
Baniso -1Baniso -2Baniso -3
1--0.195 Å2-0 Å2-0 Å2
2---0.195 Å2-0 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 82 156 2077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131984
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181663
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.7082729
X-RAY DIFFRACTIONr_angle_other_deg1.5461.5773800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9215248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.53822.55886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40815246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.674158
X-RAY DIFFRACTIONr_chiral_restr0.1990.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02473
X-RAY DIFFRACTIONr_nbd_refined0.2010.2357
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21540
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2953
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.2950
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2114
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.217
X-RAY DIFFRACTIONr_nbd_other0.1980.290
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.214
X-RAY DIFFRACTIONr_mcbond_it2.6482.79997
X-RAY DIFFRACTIONr_mcbond_other2.6452.786996
X-RAY DIFFRACTIONr_mcangle_it3.974.151241
X-RAY DIFFRACTIONr_mcangle_other3.9684.1551242
X-RAY DIFFRACTIONr_scbond_it3.0983.055987
X-RAY DIFFRACTIONr_scbond_other3.0713.018943
X-RAY DIFFRACTIONr_scangle_it4.664.4811484
X-RAY DIFFRACTIONr_scangle_other4.6674.4151419
X-RAY DIFFRACTIONr_lrange_it6.61932.8592288
X-RAY DIFFRACTIONr_lrange_other6.51932.1392190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.251970.1982060X-RAY DIFFRACTION99.9537
1.847-1.8970.236990.2021991X-RAY DIFFRACTION100
1.897-1.9520.2691010.2141942X-RAY DIFFRACTION100
1.952-2.0120.2191010.1831916X-RAY DIFFRACTION100
2.012-2.0780.224900.1811828X-RAY DIFFRACTION100
2.078-2.1510.2221000.1811784X-RAY DIFFRACTION100
2.151-2.2320.234880.191715X-RAY DIFFRACTION100
2.232-2.3240.254780.1951669X-RAY DIFFRACTION100
2.324-2.4270.172830.1771583X-RAY DIFFRACTION100
2.427-2.5450.211930.1781523X-RAY DIFFRACTION100
2.545-2.6830.246830.1831459X-RAY DIFFRACTION100
2.683-2.8450.225700.1781394X-RAY DIFFRACTION100
2.845-3.0420.194690.1721289X-RAY DIFFRACTION100
3.042-3.2850.229440.1781259X-RAY DIFFRACTION100
3.285-3.5980.218650.1941113X-RAY DIFFRACTION100
3.598-4.0220.212520.1741043X-RAY DIFFRACTION100
4.022-4.6430.169520.147906X-RAY DIFFRACTION100
4.643-5.6840.226380.15795X-RAY DIFFRACTION100
5.684-8.0260.224270.196639X-RAY DIFFRACTION100

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