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- PDB-7r4u: Apoform of FtrA/P19 from Rubrivivax gelatinosus -

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Basic information

Entry
Database: PDB / ID: 7r4u
TitleApoform of FtrA/P19 from Rubrivivax gelatinosus
ComponentsFtrA-P19
KeywordsTRANSPORT PROTEIN / Copper binding / iron transport
Biological speciesRubrivivax gelatinosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.23 Å
AuthorsMorera, S. / Vigouroux, A. / Plancqueel, S.
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 9, 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)36,97012
Polymers36,3792
Non-polymers59110
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-113 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.340, 79.970, 82.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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(DE3) (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 2M AS, 0.1 M NaCitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979336 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979336 Å / Relative weight: 1
ReflectionResolution: 1.23→48.25 Å / Num. obs: 114401 / % possible obs: 98.9 % / Redundancy: 12.77 % / Biso Wilson estimate: 17.26 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18.9
Reflection shellResolution: 1.23→1.3 Å / Rmerge(I) obs: 2 / Num. unique obs: 17537 / CC1/2: 0.424

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Phasing

PhasingMethod: molecular replacement

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Processing

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

7r3p


Resolution: 1.23→48.25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.968 / SU R Cruickshank DPI: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.039 / SU Rfree Blow DPI: 0.04 / SU Rfree Cruickshank DPI: 0.037
RfactorNum. reflection% reflectionSelection details
Rfree0.186 5717 5 %RANDOM
Rwork0.17 ---
obs0.171 114347 98.8 %-
Displacement parametersBiso max: 97.9 Å2 / Biso mean: 22.84 Å2 / Biso min: 10.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.2347 Å20 Å20 Å2
2---1.0217 Å20 Å2
3---1.2565 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: final / Resolution: 1.23→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 31 394 2938
Biso mean--40.19 36.69 -
Num. residues----319
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d917SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes473HARMONIC5
X-RAY DIFFRACTIONt_it2770HARMONIC20
X-RAY DIFFRACTIONt_nbd9SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion345SEMIHARMONIC5
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_contact3413SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2770HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3792HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion5.08
X-RAY DIFFRACTIONt_other_torsion15.08
LS refinement shellResolution: 1.23→1.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3251 113 4.94 %
Rwork0.3322 2174 -
all0.3318 2287 -
obs--77.82 %
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)
10.55890.1403-0.18590.3733-0.08730.44690.0056-0.0055-0.06390.0093-0.00820.01230.0311-0.00670.0026-0.04370.0028-0.0072-0.03940.003-0.02720.1493-26.3914-3.5813
20.3708-0.11570.05720.763-0.39550.59640.01820.09310.0425-0.0941-0.0584-0.031-0.04270.04040.04020.10190.00570.00170.10050.01130.087113.9042-10.0132-18.0789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 155
2X-RAY DIFFRACTION2{ B|* }B0 - 162

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