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- PDB-7r3s: FtrA/P19 of Rubrivivax gelatinosus in complex with Ni -

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Basic information

Entry
Database: PDB / ID: 7r3s
TitleFtrA/P19 of Rubrivivax gelatinosus in complex with Ni
ComponentsFtrA-P19 protein
KeywordsTRANSPORT PROTEIN / COPPER BINDING / IRON TRANSPORT
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciesRubrivivax gelatinosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 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 7, 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 protein
B: FtrA-P19 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4339
Polymers38,9482
Non-polymers4857
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-88 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.280, 79.810, 82.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FtrA-P19 protein


Mass: 19473.951 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)

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Non-polymers , 5 types, 232 molecules

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


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 2M AS, 0.1 M Citrate Sodium, 0.02 M NiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.48484 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48484 Å / Relative weight: 1
ReflectionResolution: 1.79→47.59 Å / Num. obs: 68702 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 35.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.2
Reflection shellResolution: 1.79→1.9 Å / Num. unique obs: 10524 / CC1/2: 0.561

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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: 1.79→47.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.1
RfactorNum. reflection% reflectionSelection details
Rfree0.201 1842 5 %RANDOM
Rwork0.176 ---
obs0.177 36839 99 %-
Displacement parametersBiso max: 122.73 Å2 / Biso mean: 39.3 Å2 / Biso min: 21.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.3416 Å20 Å20 Å2
2---2.3274 Å20 Å2
3---2.669 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.79→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2491 0 24 225 2740
Biso mean--57.38 48.42 -
Num. residues----316
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d888SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes458HARMONIC5
X-RAY DIFFRACTIONt_it2692HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion337SEMIHARMONIC5
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_contact3168SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2692HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3680HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.15
X-RAY DIFFRACTIONt_other_torsion16.57
LS refinement shellResolution: 1.79→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3208 36 4.88 %
Rwork0.328 701 -
all0.3276 737 -
obs--77.1 %
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)
11.57040.2444-0.31210.7095-0.19630.7557-0.00060.0145-0.15890.0259-0.01730.02610.05870.00870.0179-0.1010.0104-0.0176-0.127-0.0008-0.11650.1493-26.3914-3.5813
21.43170.02490.05521.243-0.45611.3632-0.0230.30740.204-0.1434-0.05-0.0443-0.14120.09040.07290.0238-0.0033-0.01010.04430.0463-0.002813.9042-10.0132-18.0789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 158
2X-RAY DIFFRACTION2{ B|* }B0 - 156

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