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- PDB-6d57: Campylobacter jejuni ferric uptake regulator S1 metalated -

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Basic information

Entry
Database: PDB / ID: 6d57
TitleCampylobacter jejuni ferric uptake regulator S1 metalated
ComponentsFerric uptake regulation protein
KeywordsMETAL TRANSPORT / Fur / ferric uptake regulator / Campylobacter jejuni / metalloregulator
Function / homology
Function and homology information


DNA-binding transcription factor activity / 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
FORMIC ACID / Fur family transcriptional regulator
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å
AuthorsSarvan, S. / Brunzelle, J.S. / Couture, J.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Sci Rep / Year: 2018
Title: Functional insights into the interplay between DNA interaction and metal coordination in ferric uptake regulators.
Authors: Sarvan, S. / Charih, F. / Askoura, M. / Butcher, J. / Brunzelle, J.S. / Stintzi, A. / Couture, J.F.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)37,59815
Polymers36,8232
Non-polymers77513
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-37 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.742, 84.363, 123.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ferric uptake regulation protein / Fur


Mass: 18411.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter)
Gene: fur, A0L11_08850, A8118_04250, AJ878_05735, AJY51_02300, AJY53_01130, AJY73_06030, B5Y32_02790, B5Z71_06080, BD28_01920, BKM79_01965, CRM98_01485
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E7PHN7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris, pH 5.5, 0.25 M magnesium formate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→69.68 Å / Num. obs: 34641 / % possible obs: 100 % / Redundancy: 3.4 % / Biso Wilson estimate: 20.49 Å2 / Net I/σ(I): 5.3
Reflection shellResolution: 1.81→1.9 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.81→69.68 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.118
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1742 5.03 %RANDOM
Rwork0.184 ---
obs0.186 34641 98.9 %-
Displacement parametersBiso mean: 27.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.4095 Å20 Å20 Å2
2---0.1382 Å20 Å2
3----1.2713 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: LAST / Resolution: 1.81→69.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 44 398 2811
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0162445HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.33268HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d882SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes343HARMONIC5
X-RAY DIFFRACTIONt_it2445HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion17.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3103SEMIHARMONIC4
LS refinement shellResolution: 1.81→1.87 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2533 148 5.25 %
Rwork0.2182 2672 -
all0.2199 2820 -
obs--98.87 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6845-0.5369-0.3540.60010.87121.6142-0.00930.0714-0.00540.06480.06090.00190.223-0.0377-0.0516-0.0084-0.0331-0.0065-0.04410.0218-0.057512.496695.3018133.701
20.57110.4494-0.08760.7553-0.14960.44850.0408-0.0987-0.10260.2082-0.05550.00490.00130.04420.0147-0.0224-0.00440.0035-0.03730.0162-0.03489.965898.8587156.837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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