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- PDB-8gog: Structure of streptavidin mutant (S112Y-K121E) complexed with bio... -

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Basic information

Entry
Database: PDB / ID: 8gog
TitleStructure of streptavidin mutant (S112Y-K121E) complexed with biotin-cyclopentadienyl-rhodium (III)(Cp*-Rh(III))
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / Streptavidin / Biotin / Rhodium / Enantioselectivity / Protein Engineering / Enzyme
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
: / RHODIUM(III) ION / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSairaman, A. / Mukherjee, P. / Maiti, D. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB) India
CitationJournal: Nat Synth / Year: 2024
Title: Enantiodivergent synthesis of isoindolones catalysed by a Rh(III)-based artificial metalloenzyme
Authors: Mukherjee, P. / Sairaman, A. / Deka, H.J. / Jain, S. / Mishra, S.K. / Roy, S. / Bhaumik, P. / Maiti, D.
History
DepositionAug 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author / Item: _citation.journal_abbrev / _citation.journal_id_CSD
Revision 1.2May 15, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,77826
Polymers25,7162
Non-polymers3,06224
Water1,18966
1
A: Streptavidin
B: Streptavidin
hetero molecules

A: Streptavidin
B: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,55652
Polymers51,4314
Non-polymers6,12548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area10820 Å2
ΔGint-125 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.450, 81.390, 90.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Streptavidin


Mass: 12857.785 Da / Num. of mol.: 2 / Mutation: S112Y,K121E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629

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Non-polymers , 6 types, 90 molecules

#2: Chemical
ChemComp-RH3 / RHODIUM(III) ION


Mass: 102.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rh
#3: Chemical ChemComp-JSU / trichloro((3~{a}~{S},4~{S},6~{a}~{R})-4-[(5~{R})-5-oxidanyl-5-[2-(2,3,4,5-tetramethylcyclopenta-2,4-dien-1-ylidene)ethylamino]pentyl]-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-2-one)rhodium(3+)


Mass: 599.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32Cl3N3O2RhS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.7 / Details: 0.2 M sodium sulfate pH 6.7 with 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 19868 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.31 / Net I/σ(I): 4
Reflection shellResolution: 2→2.1 Å / Num. unique obs: 2711 / CC1/2: 0.53

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CSE

5cse


Resolution: 2→39.73 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2942 992 5 %RANDOM
Rwork0.251 ---
obs0.2532 19843 98.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 145 66 2031
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.312
X-RAY DIFFRACTIONf_dihedral_angle_d10.875318
X-RAY DIFFRACTIONf_chiral_restr0.076310
X-RAY DIFFRACTIONf_plane_restr0.009332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.110.24251430.20052711X-RAY DIFFRACTION100
2.11-2.240.23031400.18012659X-RAY DIFFRACTION100
2.24-2.410.29761430.23022706X-RAY DIFFRACTION100
2.41-2.650.33411410.26352684X-RAY DIFFRACTION99
2.65-3.040.28271420.24842688X-RAY DIFFRACTION98
3.04-3.820.32721410.25622682X-RAY DIFFRACTION97

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