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

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Basic information

Entry
Database: PDB / ID: 7knl
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, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile.
Similarity search - Domain/homology
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMiller, K.R. / Follmer, A.H. / Jasniewski, A.J. / Sabuncu, S. / Biswas, S. / Albert, T. / Biswas, A. / 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
DepositionNov 4, 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


Theoretical massNumber of molelcules
Total (without water)16,5621
Polymers16,5621
Non-polymers00
Water1,13563
1
A: Streptavidin

A: Streptavidin

A: Streptavidin

A: Streptavidin


Theoretical massNumber of molelcules
Total (without water)66,2484
Polymers66,2484
Non-polymers00
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 area8600 Å2
ΔGint-46 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.644, 57.644, 171.909
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-208-

HOH

21A-221-

HOH

31A-256-

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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 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: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→40.76 Å / Num. obs: 32429 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.009 / Rrim(I) all: 0.033 / Net I/σ(I): 38.3 / Num. measured all: 445698 / Scaling rejects: 8
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
1.35-1.3713.60.9772165015930.8790.2751.0162.899.9
7.39-40.76120.024300625010.0070.02594.599.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCB

2qcb


Resolution: 1.35→40.67 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.888 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 1694 5.2 %RANDOM
Rwork0.216 ---
obs0.2173 30695 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.83 Å2 / Biso mean: 23.045 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refinement stepCycle: final / Resolution: 1.35→40.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 0 63 1000
Biso mean---34.55 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121034
X-RAY DIFFRACTIONr_bond_other_d0.0010.018868
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.6491429
X-RAY DIFFRACTIONr_angle_other_deg1.6371.5732018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0965141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.04822.07553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92215142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.653156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021238
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02248
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 124 -
Rwork0.432 2228 -
all-2352 -
obs--99.92 %

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