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

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Basic information

Entry
Database: PDB / ID: 5wba
TitlePeroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - WT
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
ACETATE ION / COPPER (II) ION / Chem-SI8 / 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.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM50781-21S1 United States
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 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3825
Polymers16,5701
Non-polymers8124
Water1,892105
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,52820
Polymers66,2804
Non-polymers3,24716
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-86 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.510, 57.510, 183.130
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-324-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Streptavidin


Mass: 16570.018 Da / Num. of mol.: 1 / Fragment: UNP residues 38-183
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, 109 molecules

#2: Chemical ChemComp-SI8 / [N-(2-{bis[2-(pyridin-2-yl-kappaN)ethyl]amino-kappaN}ethyl)-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamide](hydrogen peroxido-kappaO)copper


Mass: 593.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H37CuN6O4S
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M sodium acetate, pH 4.0, 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: May 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: 1.5→54.87 Å / Num. obs: 24121 / % possible obs: 95.8 % / Redundancy: 7 % / Net I/σ(I): 20.2
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→54.87 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.659 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.051 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15135 1199 5 %RANDOM
Rwork0.14034 ---
obs0.14089 22891 95.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.598 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.5→54.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 48 105 1089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021023
X-RAY DIFFRACTIONr_bond_other_d0.0020.02839
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9661398
X-RAY DIFFRACTIONr_angle_other_deg0.88631934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.20823.57142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32115135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.988155
X-RAY DIFFRACTIONr_chiral_restr0.0880.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021149
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02224
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_it1.2271.697504
X-RAY DIFFRACTIONr_mcbond_other0.9971.687502
X-RAY DIFFRACTIONr_mcangle_it1.5472.53628
X-RAY DIFFRACTIONr_mcangle_other1.6262.537629
X-RAY DIFFRACTIONr_scbond_it1.2342.013519
X-RAY DIFFRACTIONr_scbond_other1.2332.001516
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4942.86762
X-RAY DIFFRACTIONr_long_range_B_refined2.44721.2751152
X-RAY DIFFRACTIONr_long_range_B_other2.46521.1921150
X-RAY DIFFRACTIONr_rigid_bond_restr0.98631860
X-RAY DIFFRACTIONr_sphericity_free21.632575
X-RAY DIFFRACTIONr_sphericity_bonded5.02351865
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 49 -
Rwork0.218 1270 -
obs--72 %

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