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- PDB-6h1c: Structure of Ferric uptake regulator from Pseudomonas aeruginosa ... -

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Basic information

Entry
Database: PDB / ID: 6h1c
TitleStructure of Ferric uptake regulator from Pseudomonas aeruginosa with manganese.
ComponentsFerric uptake regulation protein
KeywordsTRANSCRIPTION / Ferric uptake regulator
Function / homology
Function and homology information


negative regulation of siderophore biosynthetic process / siderophore biosynthetic process / DNA-binding transcription repressor activity / protein-DNA complex / ferrous iron binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / zinc ion binding / cytosol
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 speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsNader, S. / Perard, J. / Carpentier, P. / Michaud-Soret, I. / Crouzy, S.
CitationJournal: To Be Published
Title: Ferric uptake regulator with Mn and Zn form Pseudomonas aeruginosa
Authors: Nader, S. / Perard, J. / Carpentier, P. / Michaud-Soret, I. / Crouzy, S.
History
DepositionJul 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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)31,64025
Polymers30,2512
Non-polymers1,38923
Water1,910106
1
A: Ferric uptake regulation protein
hetero molecules

A: Ferric uptake regulation protein
hetero molecules

B: Ferric uptake regulation protein
hetero molecules

B: Ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,28050
Polymers60,5014
Non-polymers2,77846
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
crystal symmetry operation5_554y,-x+y,z-1/61
crystal symmetry operation7_565y,x+1,-z+1/31
Buried area15590 Å2
ΔGint-881 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.570, 85.570, 179.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-203-

MN

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Components

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


Mass: 15125.369 Da / Num. of mol.: 2 / Mutation: H86A, H124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 / Gene: fur, PA4764 / Plasmid: pET30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03456
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100mM MES pH 6 10mM MnCl2 20% PEG 8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.96, 1.29
DetectorType: DECTRIS PILATUS3 R CdTe 300K-W / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961
21.291
ReflectionResolution: 2.199→46.12 Å / Num. obs: 20008 / % possible obs: 99.73 % / Redundancy: 3 % / Net I/σ(I): 7.61
Reflection shellResolution: 2.199→2.278 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MZB

1mzb


Resolution: 2.34→46.12 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.31
RfactorNum. reflection% reflection
Rfree0.2681 804 4.72 %
Rwork0.2009 --
obs0.2041 17023 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.34→46.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 23 106 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082122
X-RAY DIFFRACTIONf_angle_d0.8612852
X-RAY DIFFRACTIONf_dihedral_angle_d12.8941293
X-RAY DIFFRACTIONf_chiral_restr0.05323
X-RAY DIFFRACTIONf_plane_restr0.004375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3402-2.48680.34441290.2932647X-RAY DIFFRACTION100
2.4868-2.67880.35071270.26542674X-RAY DIFFRACTION100
2.6788-2.94840.29091360.23952664X-RAY DIFFRACTION100
2.9484-3.3750.27781440.20092682X-RAY DIFFRACTION100
3.375-4.25210.27761330.1652625X-RAY DIFFRACTION96
4.2521-68.53390.21051350.17452927X-RAY DIFFRACTION100

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