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- PDB-3eyy: Structural basis for the specialization of Nur, a nickel-specific... -

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Basic information

Entry
Database: PDB / ID: 3eyy
TitleStructural basis for the specialization of Nur, a nickel-specific Fur homologue, in metal sensing and DNA recognition
ComponentsPutative iron uptake regulatory protein
KeywordsTRANSPORT / Nur / nickel-uptake regulator / D-domain / dimerization domain / DB-domain / DNA-binding domain
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 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
MALONATE ION / NICKEL (II) ION / Iron uptake regulatory protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCha, S.-S. / An, Y.J.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Structural basis for the specialization of Nur, a nickel-specific Fur homolog, in metal sensing and DNA recognition
Authors: An, Y.J. / Ahn, B.-E. / Han, A.-R. / Kim, H.-M. / Chung, K.M. / Shin, J.-H. / Cho, Y.-B. / Roe, J.-H. / Cha, S.-S.
History
DepositionOct 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: 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_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.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_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

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Assembly

Deposited unit
A: Putative iron uptake regulatory protein
B: Putative iron uptake regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,48818
Polymers32,5092
Non-polymers98016
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-28 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.164, 79.164, 49.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative iron uptake regulatory protein


Mass: 16254.288 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K4F8

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Non-polymers , 6 types, 98 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 296.15 K / Method: microbatch / pH: 7
Details: 14% PEG 3350, 0.4M sodium malonate (pH 7), 0.1mM benzamidine hydrochloride, 0.1mM NiCl2, pH 7.0, Microbatch, temperature 296.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.4847, 1.4857, 1.4510
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 6, 2007
RadiationMonochromator: Ni MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.48471
21.48571
31.4511
ReflectionResolution: 2.4→50 Å / Num. obs: 18205 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 27.5 Å2
Reflection shellHighest resolution: 2.4 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.79 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1031976.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 655 5 %RANDOM
Rwork0.218 ---
obs0.218 13008 95.8 %-
all-13583 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.0547 Å2 / ksol: 0.310493 e/Å3
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å22.59 Å20 Å2
2--2.46 Å20 Å2
3----4.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 46 82 2088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 102 5.1 %
Rwork0.28 1904 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4mal.parammal.top
X-RAY DIFFRACTION5edo.paramedo.top

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