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- PDB-5wbc: Designed Artificial Cupredoxins - WT -

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Basic information

Entry
Database: PDB / ID: 5wbc
TitleDesigned Artificial Cupredoxins - WT
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / beta barrel / cupredoxin / copper complex / artificial metalloprotein / 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 ...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
ACETATE ION / [CuII(biot-et-dpea)]2+ / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMann, S.I. / Heinisch, T. / Weitz, A.C. / Hendrich, M.R. / Ward, T.R. / Borovik, A.S.
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Modular Artificial Cupredoxins.
Authors: Mann, S.I. / Heinisch, T. / Weitz, A.C. / Hendrich, M.P. / Ward, T.R. / Borovik, A.S.
History
DepositionJun 28, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 16, 2017ID: 5K49
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3134
Polymers16,5701
Non-polymers7433
Water1,04558
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,25316
Polymers66,2804
Non-polymers2,97312
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 area11280 Å2
ΔGint-50 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.580, 57.580, 183.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

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Components

#1: Protein Streptavidin


Mass: 16570.018 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
#2: Chemical ChemComp-CU6 / [CuII(biot-et-dpea)]2+


Mass: 592.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36CuN6O4S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 274 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M sodium acetate, pH 4, 2.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→54.94 Å / Num. obs: 16931 / % possible obs: 99.7 % / Redundancy: 7.9 % / CC1/2: 1 / Net I/σ(I): 12
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.108 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QCB

2qcb


Resolution: 1.72→54.94 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.999 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16788 834 4.9 %RANDOM
Rwork0.13416 ---
obs0.13601 16072 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.139 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.72→54.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 48 58 1030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.021005
X-RAY DIFFRACTIONr_bond_other_d0.0050.02850
X-RAY DIFFRACTIONr_angle_refined_deg2.5842.0451373
X-RAY DIFFRACTIONr_angle_other_deg1.13931941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2235124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.1623.65941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3715131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.812155
X-RAY DIFFRACTIONr_chiral_restr0.1530.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021148
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02241
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_it3.1261.786496
X-RAY DIFFRACTIONr_mcbond_other3.0021.775495
X-RAY DIFFRACTIONr_mcangle_it3.9752.664620
X-RAY DIFFRACTIONr_mcangle_other3.9872.675621
X-RAY DIFFRACTIONr_scbond_it5.7012.254506
X-RAY DIFFRACTIONr_scbond_other5.7022.263507
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1633.213751
X-RAY DIFFRACTIONr_long_range_B_refined5.82416.0721127
X-RAY DIFFRACTIONr_long_range_B_other5.80516.0751127
X-RAY DIFFRACTIONr_rigid_bond_restr4.96231850
X-RAY DIFFRACTIONr_sphericity_free22.272520
X-RAY DIFFRACTIONr_sphericity_bonded13.95951868
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 55 -
Rwork0.229 1162 -
obs--98.7 %

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