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- PDB-5nbc: Structure of Prokaryotic Transcription Factors -

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Basic information

Entry
Database: PDB / ID: 5nbc
TitleStructure of Prokaryotic Transcription Factors
ComponentsFerric uptake regulation protein
KeywordsDNA BINDING PROTEIN / Virulence factor
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding / cytoplasm
Similarity search - Function
Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich ...Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Ferric uptake regulation protein / Ferric uptake regulation protein
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.699 Å
AuthorsPerard, J. / Carpentier, P. / Michaud-Soret, I. / Cavazza, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BS07-0007 PepSiFUR France
CitationJournal: Commun Biol / Year: 2018
Title: Structural and functional studies of the metalloregulator Fur identify a promoter-binding mechanism and its role inFrancisella tularensisvirulence.
Authors: Perard, J. / Nader, S. / Levert, M. / Arnaud, L. / Carpentier, P. / Siebert, C. / Blanquet, F. / Cavazza, C. / Renesto, P. / Schneider, D. / Maurin, M. / Coves, J. / Crouzy, S. / Michaud-Soret, I.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev ...audit_author / database_PDB_rev / database_PDB_rev_record / entity
Item: _audit_author.name / _entity.formula_weight
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferric uptake regulation protein
B: Ferric uptake regulation protein
C: Ferric uptake regulation protein
D: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,16012
Polymers64,6794
Non-polymers4818
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9000 Å2
ΔGint-50 kcal/mol
Surface area25020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.150, 90.000, 63.950
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ferric uptake regulation protein


Mass: 16169.630 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: fur, AV531_00680, DR86_1441 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZLC3, UniProt: Q5NIN6*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M MES pH 5.8, 20% W/V PEG 3350 0.2 M Magnesium chlorides hexahydrate 0,01mM of MnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97, 1.77
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
21.771
ReflectionResolution: 1.69→42.08 Å / Num. obs: 64620 / % possible obs: 97.7 % / Redundancy: 3.6 % / Net I/σ(I): 11.66

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XSCALEVERSION November 3, 2014 BUILT=20141118data scaling
SHELXCDVERSION 2014/2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.699→42.076 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 3194 4.95 %
Rwork0.2153 --
obs0.2167 64585 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→42.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4087 0 8 402 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074211
X-RAY DIFFRACTIONf_angle_d0.8745663
X-RAY DIFFRACTIONf_dihedral_angle_d16.9651603
X-RAY DIFFRACTIONf_chiral_restr0.053629
X-RAY DIFFRACTIONf_plane_restr0.005730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6993-1.72470.3441360.31882150X-RAY DIFFRACTION80
1.7247-1.75160.32771070.29432426X-RAY DIFFRACTION89
1.7516-1.78030.31571300.29092508X-RAY DIFFRACTION93
1.7803-1.8110.32381240.2722633X-RAY DIFFRACTION97
1.811-1.8440.3111510.26412701X-RAY DIFFRACTION100
1.844-1.87940.29041400.25222742X-RAY DIFFRACTION100
1.8794-1.91780.29131280.24282702X-RAY DIFFRACTION100
1.9178-1.95950.27741570.23232698X-RAY DIFFRACTION100
1.9595-2.00510.2791410.22312723X-RAY DIFFRACTION100
2.0051-2.05520.24191300.21482766X-RAY DIFFRACTION100
2.0552-2.11080.24011350.20612691X-RAY DIFFRACTION100
2.1108-2.17290.25841410.20912713X-RAY DIFFRACTION100
2.1729-2.2430.22611460.2042718X-RAY DIFFRACTION100
2.243-2.32320.23781420.21282741X-RAY DIFFRACTION100
2.3232-2.41620.28021410.21232703X-RAY DIFFRACTION100
2.4162-2.52610.2591440.2172724X-RAY DIFFRACTION100
2.5261-2.65930.25371440.21432731X-RAY DIFFRACTION100
2.6593-2.82590.2451410.21882720X-RAY DIFFRACTION100
2.8259-3.0440.25671430.2112698X-RAY DIFFRACTION99
3.044-3.35020.20461450.20472764X-RAY DIFFRACTION100
3.3502-3.83470.2351430.20552695X-RAY DIFFRACTION99
3.8347-4.83020.19811440.18162729X-RAY DIFFRACTION99
4.8302-42.08840.22561410.2222715X-RAY DIFFRACTION97

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