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- PDB-7r5e: FtrA-P19 from Rubrivivax gelatinosus in complex with copper and m... -

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Basic information

Entry
Database: PDB / ID: 7r5e
TitleFtrA-P19 from Rubrivivax gelatinosus in complex with copper and magnesium (X1)
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 support1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS)
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)36,6858
Polymers36,3792
Non-polymers3066
Water2,324129
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)92.580, 48.860, 78.220
Angle α, β, γ (deg.)90.000, 123.150, 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.: 3 / 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.: 129 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 4K, 0.1 M Tris-HCl, 0.1 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.73114 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73114 Å / Relative weight: 1
ReflectionResolution: 2.2→27.42 Å / Num. obs: 14428 / % possible obs: 98.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 27.13 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.128 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.554 / Num. unique obs: 523 / CC1/2: 0.561

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7r3p


Resolution: 2.2→27.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 0.318 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.327 / SU Rfree Blow DPI: 0.205 / SU Rfree Cruickshank DPI: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.217 715 4.96 %RANDOM
Rwork0.176 ---
obs0.178 14428 95.7 %-
Displacement parametersBiso max: 99.5 Å2 / Biso mean: 23.18 Å2 / Biso min: 4.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.7903 Å20 Å2-1.6613 Å2
2--1.8726 Å20 Å2
3----0.0823 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 2.2→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 12 129 2603
Biso mean--32.23 24.42 -
Num. residues----312
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d833SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes430HARMONIC5
X-RAY DIFFRACTIONt_it2566HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion320SEMIHARMONIC5
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_contact2858SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2566HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3492HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion19.86
LS refinement shellResolution: 2.2→2.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 35
RfactorNum. reflection% reflection
Rfree0.4292 20 4.84 %
Rwork0.2397 393 -
all0.25 413 -
obs--64.87 %
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)
11.4467-0.29920.10791.19360.25110.6243-0.1047-0.40140.11750.22440.1506-0.21290.04350.1342-0.04590.050.0545-0.06030.2279-0.04830.0367-0.07193.071525.4538
22.0783-0.21110.65820.4235-0.10920.96640.09270.2688-0.2285-0.1102-0.00390.11510.1092-0.0735-0.08880.03210.0027-0.03770.096-0.02240.0463-18.1552-3.25428.3964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 156
2X-RAY DIFFRACTION2{ B|* }B0 - 156

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