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- PDB-6esu: Artificial imine reductase mutant S112A-N118P-K121A-S122M -

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Basic information

Entry
Database: PDB / ID: 6esu
TitleArtificial imine reductase mutant S112A-N118P-K121A-S122M
ComponentsStreptavidin
Keywordsbiotin-binding protein / streptavidin / beta-barrel
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 ...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-6IR / ACETATE ION / : / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsHestericova, M. / Heinisch, T. / Alonso-Cotchico, L. / Marechal, J.-D. / Vidossich, P. / Ward, T.R.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Directed Evolution of an Artificial Imine Reductase.
Authors: Hestericova, M. / Heinisch, T. / Alonso-Cotchico, L. / Marechal, J.D. / Vidossich, P. / Ward, T.R.
History
DepositionOct 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0258
Polymers16,6591
Non-polymers1,3667
Water52229
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,09932
Polymers66,6374
Non-polymers5,46228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area12510 Å2
ΔGint-169 kcal/mol
Surface area17790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.801, 57.801, 178.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Streptavidin


Mass: 16659.178 Da / Num. of mol.: 1
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 , 5 types, 36 molecules

#2: Chemical ChemComp-6IR / 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}-[4-(2-azanylethylsulfamoyl)phenyl]pentanamide


Mass: 441.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H27N5O4S2
#3: Chemical
ChemComp-IR / IRIDIUM ION


Mass: 192.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ir
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.78→55 Å / Num. obs: 15084 / % possible obs: 99.9 % / Redundancy: 25.4 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 18.7
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.098 / Mean I/σ(I) obs: 1.5 / Num. unique all: 816 / CC1/2: 0.88 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCB

2qcb


Resolution: 1.78→54.98 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.655 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21126 761 5.1 %RANDOM
Rwork0.19438 ---
obs0.19524 14300 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.32 Å20 Å20 Å2
2---2.32 Å20 Å2
3---4.64 Å2
Refinement stepCycle: 1 / Resolution: 1.78→54.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms926 0 42 29 997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02995
X-RAY DIFFRACTIONr_bond_other_d0.0020.02822
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.9371364
X-RAY DIFFRACTIONr_angle_other_deg1.04431894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6625124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.31723.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61215128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.229155
X-RAY DIFFRACTIONr_chiral_restr0.1220.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021127
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02218
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_it5.5315.086494
X-RAY DIFFRACTIONr_mcbond_other5.5065.078492
X-RAY DIFFRACTIONr_mcangle_it8.4827.6615
X-RAY DIFFRACTIONr_mcangle_other8.4757.606616
X-RAY DIFFRACTIONr_scbond_it5.7055.242500
X-RAY DIFFRACTIONr_scbond_other5.6225.23497
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.2547.695743
X-RAY DIFFRACTIONr_long_range_B_refined13.11457.2781087
X-RAY DIFFRACTIONr_long_range_B_other13.0856.9151059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.777→1.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 51 -
Rwork0.368 1016 -
obs--98.61 %

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