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- PDB-6uiy: Artificial Iron Proteins: Modelling the Active Sites in Non-Heme ... -

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Basic information

Entry
Database: PDB / ID: 6uiy
TitleArtificial Iron Proteins: Modelling the Active Sites in Non-Heme Dioxygenases
ComponentsStreptavidin
KeywordsMETAL BINDING PROTEIN / Biotin binding artificial metalloprotein
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-QG1 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsMiller, K.R. / Paretsky, J.D. / Follmer, A.H. / Heinisch, T. / Mittra, K. / Gul, S. / Kim, I.-S. / Fuller, F.D. / Batyuk, A. / Sutherlin, K.D. ...Miller, K.R. / Paretsky, J.D. / Follmer, A.H. / Heinisch, T. / Mittra, K. / Gul, S. / Kim, I.-S. / Fuller, F.D. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bhowmick, A. / Sauter, N.K. / Kern, J. / Yano, J. / Green, M.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)RO1GM120349 United States
CitationJournal: Inorg.Chem. / Year: 2020
Title: Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases.
Authors: Miller, K.R. / Paretsky, J.D. / Follmer, A.H. / Heinisch, T. / Mittra, K. / Gul, S. / Kim, I.S. / Fuller, F.D. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bhowmick, A. / Sauter, N.K. / ...Authors: Miller, K.R. / Paretsky, J.D. / Follmer, A.H. / Heinisch, T. / Mittra, K. / Gul, S. / Kim, I.S. / Fuller, F.D. / Batyuk, A. / Sutherlin, K.D. / Brewster, A.S. / Bhowmick, A. / Sauter, N.K. / Kern, J. / Yano, J. / Green, M.T. / Ward, T.R. / Borovik, A.S.
History
DepositionOct 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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)17,1964
Polymers16,5531
Non-polymers6433
Water2,126118
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,78216
Polymers66,2124
Non-polymers2,57012
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 area9910 Å2
ΔGint-60 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.740, 57.740, 184.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-202-

ACT

21A-301-

HOH

31A-331-

HOH

41A-404-

HOH

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Components

#1: Protein Streptavidin /


Mass: 16552.965 Da / Num. of mol.: 1 / Mutation: E101Q, S112E, K121A
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-QG1 / {5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-{[(pyridin-2-yl)methyl][(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)pentanamide}iron(2+)


Mass: 524.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32FeN6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 26 mg/mL protein, 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2018
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: 1.47→55.1 Å / Num. obs: 27259 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Net I/σ(I): 21.6 / Num. measured all: 351473 / Scaling rejects: 745
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.499.60.5011263713170.9280.170.5294100
8.04-55.110.20.0521862150.9970.0170.05335.998.5

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCB

2qcb


Resolution: 1.47→55.1 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1768 1383 5.1 %RANDOM
Rwork0.1528 ---
obs0.154 25837 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.08 Å2 / Biso mean: 17.436 Å2 / Biso min: 6.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 1.47→55.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 75 118 1128
Biso mean--22.87 31.27 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0131096
X-RAY DIFFRACTIONr_bond_other_d0.0380.018877
X-RAY DIFFRACTIONr_angle_refined_deg2.4341.7271499
X-RAY DIFFRACTIONr_angle_other_deg3.7251.5722027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.29822.15751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0815143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.426156
X-RAY DIFFRACTIONr_chiral_restr0.1340.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021253
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02239
LS refinement shellResolution: 1.47→1.506 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.22 102 -
Rwork0.204 1879 -
obs--100 %

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