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- PDB-7r5g: FtrA-P19 from Rubrivivax gelatinosus in complex with copper and m... -

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Basic information

Entry
Database: PDB / ID: 7r5g
TitleFtrA-P19 from Rubrivivax gelatinosus in complex with copper and magnesium (X2)
ComponentsFtrA-P19
KeywordsTRANSPORT PROTEIN / Copper binding / iron transport
Function / homologyCOPPER (II) ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesRubrivivax gelatinosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMorera, S. / Vigouroux, A.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Febs J. / Year: 2022
Title: New insights into the mechanism of iron transport through the bacterial Ftr system present in pathogens.
Authors: Steunou, A.S. / Vigouroux, A. / Aumont-Nicaise, M. / Plancqueel, S. / Boussac, A. / Ouchane, S. / Morera, S.
History
DepositionFeb 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FtrA-P19
B: FtrA-P19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6617
Polymers36,3792
Non-polymers2825
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.590, 48.360, 78.560
Angle α, β, γ (deg.)90.000, 122.760, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FtrA-P19


Mass: 18189.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubrivivax gelatinosus (bacteria) / Gene: EV684_12117
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 4K, 0.1 M Tris-HCl, 50 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.739 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.739 Å / Relative weight: 1
ReflectionResolution: 2.2→41.08 Å / Num. obs: 15041 / % possible obs: 99.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 36.77 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.23 Å / Rmerge(I) obs: 0.506 / Num. unique obs: 711 / CC1/2: 0.873

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7R3P

7r3p


Resolution: 2.2→41.08 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.274 / SU Rfree Blow DPI: 0.176 / SU Rfree Cruickshank DPI: 0.178
RfactorNum. reflection% reflectionSelection details
Rfree0.196 774 5.15 %RANDOM
Rwork0.17 ---
obs0.172 15039 99.8 %-
Displacement parametersBiso max: 114.87 Å2 / Biso mean: 34.45 Å2 / Biso min: 12.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.9952 Å20 Å2-1.9378 Å2
2---1.0888 Å20 Å2
3---0.0937 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: final / Resolution: 2.2→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 11 100 2565
Biso mean--50.09 35.04 -
Num. residues----311
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d824SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes425HARMONIC5
X-RAY DIFFRACTIONt_it2544HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
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_contact2752SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2544HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3459HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion18.36
LS refinement shellResolution: 2.2→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 38
RfactorNum. reflection% reflection
Rfree0.4476 21 5.3 %
Rwork0.2689 375 -
all0.2786 396 -
obs--96.81 %
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)
12.6848-0.44851.03561.1893-0.22861.64-0.0301-0.02980.1032-0.0038-0.0058-0.1736-0.00990.06480.0359-0.07210.0048-0.0086-0.1174-0.0045-0.0782-0.07193.071525.4537
22.1364-0.67790.57732.70960.21211.41640.05060.041-0.1828-0.4317-0.02910.36670.1143-0.0754-0.02150.20080.0007-0.07840.0658-0.00950.0892-18.1552-3.25428.3964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 156
2X-RAY DIFFRACTION2{ B|* }B2 - 155

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