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- PDB-2fu4: Crystal Structure of the DNA binding domain of E.coli FUR (Ferric... -

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Basic information

Entry
Database: PDB / ID: 2fu4
TitleCrystal Structure of the DNA binding domain of E.coli FUR (Ferric Uptake Regulator)
ComponentsFerric uptake regulation protein
KeywordsDNA BINDING PROTEIN / DNA binding domain / helix-turn-helix
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-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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Ferric uptake regulation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPecqueur, L. / D'Autreaux, B. / Dupuy, J. / Nicolet, Y. / Jacquamet, L. / Brutscher, B. / Michaud-Soret, I. / Bersch, B.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural changes of Escherichia coli ferric uptake regulator during metal-dependent dimerization and activation explored by NMR and X-ray crystallography
Authors: Pecqueur, L. / D'Autreaux, B. / Dupuy, J. / Nicolet, Y. / Jacquamet, L. / Brutscher, B. / Michaud-Soret, I. / Bersch, B.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,12023
Polymers18,7032
Non-polymers1,41721
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-158 kcal/mol
Surface area8760 Å2
MethodPISA
4
A: Ferric uptake regulation protein
B: Ferric uptake regulation protein
hetero molecules

A: Ferric uptake regulation protein
B: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,24046
Polymers37,4074
Non-polymers2,83442
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2910 Å2
ΔGint-140 kcal/mol
Surface area9520 Å2
MethodPISA
5
A: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,42216
Polymers9,3521
Non-polymers1,07115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
B: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6987
Polymers9,3521
Non-polymers3466
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.500, 159.270, 28.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 9351.656 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21List of strains of Escherichia coli / Gene: FUR(P0A9A9) / Plasmid: pET 30c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A9A9
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM sodium acetate, 30%(v/v) PEG 200 containing 100mM CdCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979637 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979637 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 17195 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.092 / Net I/σ(I): 17.72
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 22370 / Rsym value: 0.329 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XNEMOdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→37.42 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.446 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.225 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2148 863 5 %RANDOM
Rwork0.1719 ---
all0.17406 ---
obs0.17406 17195 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.613 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 26 160 1468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221338
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9751811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6525169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9632564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34715247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.406158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02994
X-RAY DIFFRACTIONr_nbd_refined0.2270.2664
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2923
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3440.2127
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0540.22
X-RAY DIFFRACTIONr_mcbond_it1.0311.5854
X-RAY DIFFRACTIONr_mcangle_it1.35321333
X-RAY DIFFRACTIONr_scbond_it2.1723536
X-RAY DIFFRACTIONr_scangle_it3.2124.5476
X-RAY DIFFRACTIONr_rigid_bond_restr1.34731390
X-RAY DIFFRACTIONr_sphericity_free5.6823180
X-RAY DIFFRACTIONr_sphericity_bonded2.27831317
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 60 -
Rwork0.176 1136 -
obs--100 %

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