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- PDB-4oka: Structural-, Kinetic- and Docking Studies of Artificial Imine Red... -

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Basic information

Entry
Database: PDB / ID: 4oka
TitleStructural-, Kinetic- and Docking Studies of Artificial Imine Reductases Based on the Biotin-Streptavidin Technology: An Induced Lock-and-Key Hypothesis
ComponentsStreptavidin
KeywordsBIOTIN-BINDING PROTEIN / beta barrel / transfer hydrogenation / iridium piano stool
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-5IR / : / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.505 Å
AuthorsSchirmer, T. / Heinisch, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Structural, Kinetic, and Docking Studies of Artificial Imine Reductases Based on Biotin-Streptavidin Technology: An Induced Lock-and-Key Hypothesis
Authors: Robles, V.M. / Durrenberger, M. / Heinisch, T. / Lledos, A. / Schirmer, T. / Ward, T.R. / Marechal, J.D.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4373
Polymers16,6121
Non-polymers8252
Water37821
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,74812
Polymers66,4484
Non-polymers3,3008
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_445-y-1,-x-1,-z1
crystal symmetry operation10_445-x-1,-y-1,z1
crystal symmetry operation15_555y,x,-z1
Buried area10110 Å2
ΔGint-79 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.605, 57.605, 183.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-502-

HOH

21A-517-

HOH

31A-519-

HOH

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Components

#1: Protein Streptavidin


Mass: 16612.119 Da / Num. of mol.: 1 / Fragment: UNP residues 38-183 / Mutation: S112K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22629
#2: Chemical ChemComp-5IR / [N-(4-{[2-(amino-kappaN)ethyl]sulfamoyl-kappaN}phenyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamidato]iridium(III)


Mass: 632.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26IrN5O4S2
#3: Chemical ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ir
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.29 Å3/Da / Density % sol: 46.26 % / Mosaicity: 0.77 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, sodium acetate, pH 8.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.36246 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36246 Å / Relative weight: 1
ReflectionResolution: 2.5→24.44 Å / Num. obs: 4971 / % possible obs: 86.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 31.21 Å2 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.5-2.641.41.52992180.16627.8
7.91-24.449.211.419872170.0696.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless3.3.20data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3pk2

3pk2


Resolution: 2.505→24.44 Å / FOM work R set: 0.8062 / SU ML: 0.3 / σ(F): 1.36 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 218 4.41 %
Rwork0.1977 --
obs0.1996 4943 87.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.22 Å2 / Biso mean: 15.76 Å2 / Biso min: 5.56 Å2
Refinement stepCycle: LAST / Resolution: 2.505→24.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 31 21 968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007987
X-RAY DIFFRACTIONf_angle_d1.3981348
X-RAY DIFFRACTIONf_chiral_restr0.068142
X-RAY DIFFRACTIONf_plane_restr0.003166
X-RAY DIFFRACTIONf_dihedral_angle_d12.043304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.505-3.15480.2865930.20461947204074
3.1548-24.44310.22191250.195227782903100

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