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- PDB-6vp3: Artificial Metalloproteins with Dinuclear Iron Centers -

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Basic information

Entry
Database: PDB / ID: 6vp3
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 / Chem-KM3 / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionFeb 1, 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 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
B: Streptavidin
C: Streptavidin
D: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,57610
Polymers66,2484
Non-polymers2,3286
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-58 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.503, 57.861, 57.861
Angle α, β, γ (deg.)90.000, 107.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-385-

HOH

21C-401-

HOH

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Components

#1: Protein
Streptavidin


Mass: 16561.932 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C26H36FeN6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→46.16 Å / Num. obs: 47899 / % possible obs: 65.2 % / Redundancy: 2.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.054 / Rrim(I) all: 0.092 / Net I/σ(I): 7.7 / Num. measured all: 114073 / Scaling rejects: 139
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
1.65-1.682.30.28479820780.9050.2050.3492.357.7
9.04-46.163.20.04710653380.9920.0310.05614.469.8

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Processing

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

2qcb


Resolution: 1.65→42.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.788 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 2442 5.1 %RANDOM
Rwork0.1761 ---
obs0.1783 45114 64.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.23 Å2 / Biso mean: 15.974 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å2-0 Å20.27 Å2
2--0.01 Å2-0 Å2
3----0.78 Å2
Refinement stepCycle: final / Resolution: 1.65→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3652 0 152 499 4303
Biso mean--22.75 31.45 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133954
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183194
X-RAY DIFFRACTIONr_angle_refined_deg2.8831.8035406
X-RAY DIFFRACTIONr_angle_other_deg1.7411.5737364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1195484
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.00922.292192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5111520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02892
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 179 -
Rwork0.232 2901 -
all-3080 -
obs--57.42 %

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