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- PDB-5wbb: Peroxide Activation Regulated by Hydrogen Bonds within Artificial... -

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Basic information

Entry
Database: PDB / ID: 5wbb
TitlePeroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - S112A
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / streptavidin / biotin / copper / hydroperoxo / secondary coordination sphere / hydrogen bond / 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
COPPER (II) ION / Chem-SQ1 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMann, S.I. / Heinisch, T. / Ward, T.R. / Borovik, A.S.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Peroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins.
Authors: Mann, S.I. / Heinisch, T. / Ward, T.R. / Borovik, A.S.
History
DepositionJun 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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)17,3665
Polymers16,5541
Non-polymers8124
Water1,982110
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,46420
Polymers66,2164
Non-polymers3,24816
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 area9890 Å2
ΔGint-87 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.640, 57.640, 183.980
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-332-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Streptavidin


Mass: 16554.018 Da / Num. of mol.: 1 / Fragment: UNP residues 38-183 / Mutation: S112A
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, 114 molecules

#2: Chemical ChemComp-SQ1 / [N-(2-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide]copper


Mass: 560.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36CuN6O2S
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#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.: 110 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M sodium acetate, 2.6 M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 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: 1.5→55 Å / Num. obs: 25455 / % possible obs: 100 % / Redundancy: 9.6 % / Net I/σ(I): 13.3
Reflection shellResolution: 1.5→1.53 Å

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Processing

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

2qcb


Resolution: 1.5→55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.459 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18803 1278 5.1 %RANDOM
Rwork0.15618 ---
obs0.15779 23945 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2---0.64 Å20 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.5→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 48 110 1094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021049
X-RAY DIFFRACTIONr_bond_other_d0.0020.02847
X-RAY DIFFRACTIONr_angle_refined_deg1.7852.1681442
X-RAY DIFFRACTIONr_angle_other_deg0.90431952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5465128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.98523.65941
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.02315135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.458155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
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_it1.6371.64509
X-RAY DIFFRACTIONr_mcbond_other1.621.632508
X-RAY DIFFRACTIONr_mcangle_it2.1582.45638
X-RAY DIFFRACTIONr_mcangle_other2.1592.458639
X-RAY DIFFRACTIONr_scbond_it2.1721.974540
X-RAY DIFFRACTIONr_scbond_other2.1681.961536
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5772.821798
X-RAY DIFFRACTIONr_long_range_B_refined3.24320.7451168
X-RAY DIFFRACTIONr_long_range_B_other3.02820.2881149
X-RAY DIFFRACTIONr_rigid_bond_restr2.66431894
X-RAY DIFFRACTIONr_sphericity_free22.88577
X-RAY DIFFRACTIONr_sphericity_bonded9.45951900
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 88 -
Rwork0.203 1740 -
obs--99.89 %

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