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- PDB-5fd6: zinc-bound manganese uptake regulator -

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Basic information

Entry
Database: PDB / ID: 5fd6
Titlezinc-bound manganese uptake regulator
ComponentsFerric uptake regulation protein
KeywordsTRANSCRIPTION / manganese uptake regulator / fur / mur / ferric uptake regulator
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
Similarity search - Component
Biological speciesRhizobium leguminosarum bv. viciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBellini, D. / Hemmings, A.M. / Walsh, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: To Be Published
Title: structure of a zinc-bound manganese uptake regulator, mur
Authors: Bellini, D. / Lebedev, A. / Keegan, R. / Todd, J. / Hemmings, A.M. / Johnston, A.W. / Walsh, M.A.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)67,94318
Polymers66,8484
Non-polymers1,09614
Water19811
1
A: Ferric uptake regulation protein
B: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,07010
Polymers33,4242
Non-polymers6468
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-77 kcal/mol
Surface area15370 Å2
MethodPISA
2
C: Ferric uptake regulation protein
D: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8748
Polymers33,4242
Non-polymers4506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-33 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.950, 94.950, 63.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 16711.914 Da / Num. of mol.: 4 / Fragment: UNP residues 2-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum bv. viciae (bacteria)
Gene: fur / Production host: Escherichia coli (E. coli) / References: UniProt: O07315
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Trizma, pH 8.0, 1.5 M ammonium sulfate. The protein sample contained a 10:1 molar excess of Zn(II)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.68
11-H, K, -L20.32
ReflectionResolution: 2.5→94.9 Å / Num. obs: 19841 / % possible obs: 99.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 9.1
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→42.46 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.583 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 993 5 %RANDOM
Rwork0.18724 ---
obs0.18891 19064 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.556 Å2
Baniso -1Baniso -2Baniso -3
1-7.19 Å20 Å20 Å2
2--7.19 Å20 Å2
3----14.38 Å2
Refinement stepCycle: LAST / Resolution: 2.48→42.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 39 11 4450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194497
X-RAY DIFFRACTIONr_bond_other_d0.0040.024350
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9716053
X-RAY DIFFRACTIONr_angle_other_deg0.93239980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.25622.195246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9915846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0281566
X-RAY DIFFRACTIONr_chiral_restr0.0730.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021048
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9946.5772124
X-RAY DIFFRACTIONr_mcbond_other3.9896.5772123
X-RAY DIFFRACTIONr_mcangle_it6.1199.8582648
X-RAY DIFFRACTIONr_mcangle_other6.1199.8582649
X-RAY DIFFRACTIONr_scbond_it3.9837.0432373
X-RAY DIFFRACTIONr_scbond_other3.9837.0432373
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3110.3783406
X-RAY DIFFRACTIONr_long_range_B_refined9.71550.5814866
X-RAY DIFFRACTIONr_long_range_B_other9.71550.5824866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.478→2.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 106 -
Rwork0.217 1354 -
obs--98.58 %

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