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- PDB-8j6w: Full length crystal structure of Escherichia coli Fur -

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Basic information

Entry
Database: PDB / ID: 8j6w
TitleFull length crystal structure of Escherichia coli Fur
ComponentsFerric uptake regulation protein
KeywordsDNA BINDING PROTEIN / ferric uptake regulator
Function / homology
Function and homology information


negative regulation of siderophore biosynthetic process / DNA-binding transcription repressor activity / DNA-binding transcription activator activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / zinc ion binding / cytosol
Similarity search - Function
Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Ferric uptake regulation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsZhang, F. / Wang, X. / Gu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Full length crystal structure of Escherichia coli Fur
Authors: Zhang, F. / Wang, X.
History
DepositionApr 26, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0865
Polymers16,8241
Non-polymers2624
Water724
1
A: Ferric uptake regulation protein
hetero molecules

A: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,17110
Polymers33,6482
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3140 Å2
ΔGint-139 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.222, 69.222, 73.273
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

#1: Protein Ferric uptake regulation protein / Ferric uptake regulator


Mass: 16823.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: fur, b0683, JW0669 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9A9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.61 Å3/Da / Density % sol: 52.85 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Potassium chloride,0.01M Magnesium chloride hexahydrate,0.05M MSA monohydrate,5%w/vPolyethylene glycol,pH=5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.66→32.38 Å / Num. obs: 5436 / % possible obs: 99.6 % / Redundancy: 1 % / Biso Wilson estimate: 64.79 Å2 / CC1/2: 0.995 / Net I/σ(I): 32.6
Reflection shellResolution: 2.66→2.79 Å / Mean I/σ(I) obs: 6.7 / Num. unique obs: 690 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→32.38 Å / SU ML: 0.3862 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 34.2284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.289 390 7.28 %
Rwork0.241 4968 -
obs0.2444 5358 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 4 4 1163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00941176
X-RAY DIFFRACTIONf_angle_d1.16641585
X-RAY DIFFRACTIONf_chiral_restr0.0721173
X-RAY DIFFRACTIONf_plane_restr0.0066211
X-RAY DIFFRACTIONf_dihedral_angle_d18.2615435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-3.050.36891140.2991580X-RAY DIFFRACTION96.09
3.05-3.840.36341430.28281636X-RAY DIFFRACTION99.11
3.84-32.380.2351330.21221752X-RAY DIFFRACTION99.26

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