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- PDB-9ire: CRYSTAL STRUCTURE OF Bacillus cereus FERRIC UPTAKE REGULATOR -

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Basic information

Entry
Database: PDB / ID: 9ire
TitleCRYSTAL STRUCTURE OF Bacillus cereus FERRIC UPTAKE REGULATOR
ComponentsFerric uptake regulation protein
KeywordsMETAL BINDING PROTEIN / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


regulation of secondary metabolite biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / zinc ion binding
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 speciesBacillus cereus VD154 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGabdulkhakov, A.G. / Tishchenko, T.V. / Kostareva, O.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF Bacillus cereus FERRIC UPTAKE REGULATOR
Authors: Gabdulkhakov, A.G. / Tishchenko, T.V. / Kostareva, O.S.
History
DepositionJul 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: 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
B: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6307
Polymers35,3442
Non-polymers2865
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-36 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.009, 99.009, 61.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

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Components

#1: Protein Ferric uptake regulation protein


Mass: 17671.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus VD154 (bacteria) / Gene: IK5_03667 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9W5KVA6
#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 200mM CaCl2, 100mM MES, pH 6.5, 33% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3→45 Å / Num. obs: 6452 / % possible obs: 99.7 % / Redundancy: 8.26 % / Biso Wilson estimate: 90.79 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.14 / Net I/σ(I): 13.08
Reflection shellResolution: 3→3.18 Å / Mean I/σ(I) obs: 1.07 / Num. unique obs: 991 / CC1/2: 0.35 / Rrim(I) all: 2.24

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→44.28 Å / SU ML: 0.371 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.3097
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2923 291 4.51 %
Rwork0.2141 6157 -
obs0.2175 6448 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.71 Å2
Refinement stepCycle: LAST / Resolution: 3→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 5 0 2424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01252456
X-RAY DIFFRACTIONf_angle_d1.49273301
X-RAY DIFFRACTIONf_chiral_restr0.0693366
X-RAY DIFFRACTIONf_plane_restr0.0421430
X-RAY DIFFRACTIONf_dihedral_angle_d19.9984946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.780.30041550.23922979X-RAY DIFFRACTION99.59
3.78-44.280.28911360.20583178X-RAY DIFFRACTION99.73

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