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- PDB-7kby: Artificial Metalloproteins with Dinuclear Iron Centers -

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Basic information

Entry
Database: PDB / ID: 7kby
TitleArtificial Metalloproteins with Dinuclear Iron Centers
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 ...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 / CYANIDE ION / Chem-KM3 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMiller, K.R. / Follmer, A.H. / Jasniewski, A.J. / Sabuncu, S. / Biswas, S. / Albert, T. / Hendrich, M.P. / Moenne-Loccoz, P. / Borovik, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120349 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Artificial Metalloproteins with Dinuclear Iron-Hydroxido Centers.
Authors: Miller, K.R. / Biswas, S. / Jasniewski, A. / Follmer, A.H. / Biswas, A. / Albert, T. / Sabuncu, S. / Bominaar, E.L. / Hendrich, M.P. / Moenne-Loccoz, P. / Borovik, A.S.
History
DepositionOct 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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)17,2004
Polymers16,5621
Non-polymers6383
Water1,26170
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,79816
Polymers66,2484
Non-polymers2,55012
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
Unit cell
Length a, b, c (Å)57.560, 57.560, 183.450
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-203-

ACT

21A-203-

ACT

31A-301-

HOH

41A-318-

HOH

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Components

#1: Protein Streptavidin


Mass: 16561.932 Da / Num. of mol.: 1 / Mutation: K121A, L124Y
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-KM3 / {N-(4-{bis[(pyridin-2-yl-kappaN)methyl]amino-kappaN}butyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}iron(3+)


Mass: 552.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H36FeN6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#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.: 70 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 26 mg/mL 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: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→45.86 Å / Num. obs: 17537 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.063 / Rrim(I) all: 0.22 / Net I/σ(I): 9.1 / Num. measured all: 205175 / Scaling rejects: 43
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
1.7-1.7311.71.84105298990.380.5491.9221.8100
9-45.8610.80.06317001580.9940.020.06726.999.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCB

2qcb


Resolution: 1.7→41.95 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 956 5.5 %RANDOM
Rwork0.1919 ---
obs0.1936 16550 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.81 Å2 / Biso mean: 20.95 Å2 / Biso min: 10.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å2-0 Å2
2---0.56 Å20 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 1.7→41.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 42 70 1040
Biso mean--34.02 31.03 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131006
X-RAY DIFFRACTIONr_bond_other_d0.0380.018816
X-RAY DIFFRACTIONr_angle_refined_deg2.6851.8021372
X-RAY DIFFRACTIONr_angle_other_deg2.961.5741879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1525123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.94121.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98515129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.118156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021144
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02230
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 65 -
Rwork0.315 1196 -
all-1261 -
obs--100 %

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