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- PDB-6anx: Peroxide Activation Regulated by Hydrogen Bonds within Artificial... -

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Basic information

Entry
Database: PDB / ID: 6anx
TitlePeroxide Activation Regulated by Hydrogen Bonds within Artificial Cu Proteins - WT (low exposure)
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Chem-SI0 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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)GM-120349 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
DepositionAug 14, 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

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Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3344
Polymers16,5701
Non-polymers7643
Water1,78399
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,33716
Polymers66,2804
Non-polymers3,05712
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 area9390 Å2
ΔGint-55 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.640, 57.640, 183.610
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

#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
#2: Chemical ChemComp-SI0 / [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)hydroxycopper


Mass: 609.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H37CuN6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


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


Mass: 18.015 Da / Num. of mol.: 99 / 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: 46.54 %
Crystal growTemperature: 274 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2.6 M ammonium sulfate, 0.1 M sodium acetate

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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: Aug 11, 2017
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: 1.62→54.99 Å / Num. obs: 20471 / % possible obs: 100 % / Redundancy: 13.4 % / Net I/σ(I): 12.9
Reflection shellResolution: 1.62→1.64 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 995 / % possible all: 99.5

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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: 1.62→54.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.617 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18691 1057 5.2 %RANDOM
Rwork0.16318 ---
obs0.16439 19386 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.085 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.62→54.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 48 99 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021024
X-RAY DIFFRACTIONr_bond_other_d0.0020.02863
X-RAY DIFFRACTIONr_angle_refined_deg2.3442.0471405
X-RAY DIFFRACTIONr_angle_other_deg1.10931972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0965128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36723.57142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70415135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.085155
X-RAY DIFFRACTIONr_chiral_restr0.130.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021169
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02248
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_it2.6091.916504
X-RAY DIFFRACTIONr_mcbond_other2.5131.903502
X-RAY DIFFRACTIONr_mcangle_it3.962.84628
X-RAY DIFFRACTIONr_mcangle_other3.9582.849629
X-RAY DIFFRACTIONr_scbond_it3.8042.302520
X-RAY DIFFRACTIONr_scbond_other3.7732.282517
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4683.254769
X-RAY DIFFRACTIONr_long_range_B_refined7.46217.0761208
X-RAY DIFFRACTIONr_long_range_B_other7.45917.11209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.615→1.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 73 -
Rwork0.311 1400 -
obs--99.33 %

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