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- PDB-7r4z: Strep-tag FtrA-P19 from Rubrivivax gelatinosus in complex with ir... -

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Basic information

Entry
Database: PDB / ID: 7r4z
TitleStrep-tag FtrA-P19 from Rubrivivax gelatinosus in complex with iron and copper
ComponentsFtrA-P19 protein
KeywordsTRANSPORT PROTEIN / Copper binding and iron transport
Function / homologyCOPPER (I) ION / :
Function and homology information
Biological speciesRubrivivax gelatinosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 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 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 protein
B: FtrA-P19 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4018
Polymers43,0512
Non-polymers3506
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-98 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.820, 71.230, 79.650
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 protein


Mass: 21525.312 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-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG2K MME, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.73925 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.73925 Å / Relative weight: 1
ReflectionResolution: 2.75→46.25 Å / Num. obs: 9026 / % possible obs: 95.5 % / Redundancy: 5.8 % / Biso Wilson estimate: 82.31 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.167 / Net I/σ(I): 10.2
Reflection shellResolution: 2.75→2.92 Å / Rmerge(I) obs: 1.072 / Num. unique obs: 1146 / CC1/2: 0.654

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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: 2.75→46.25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.327
RfactorNum. reflection% reflectionSelection details
Rfree0.226 450 5.01 %RANDOM
Rwork0.171 ---
obs0.173 8990 95.3 %-
Displacement parametersBiso max: 153.74 Å2 / Biso mean: 57.43 Å2 / Biso min: 31.61 Å2
Baniso -1Baniso -2Baniso -3
1-4.749 Å20 Å20 Å2
2---4.426 Å20 Å2
3----0.3229 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: final / Resolution: 2.75→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2462 0 6 11 2479
Biso mean--78.19 47.45 -
Num. residues----312
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d822SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes426HARMONIC5
X-RAY DIFFRACTIONt_it2546HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion318SEMIHARMONIC5
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_contact2665SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2546HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3466HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion21.05
LS refinement shellResolution: 2.75→2.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 22
RfactorNum. reflection% reflection
Rfree0.4242 21 5.13 %
Rwork0.3012 388 -
all0.3068 409 -
obs--71.73 %
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)
13.32760.4567-1.40811.04560.04032.40350.19640.08550.35760.149-0.03380.3453-0.0173-0.5789-0.1626-0.1099-0.02410.0545-0.03030.03580.1079-5.0963.895230.7435
23.0410.3262-0.91841.3068-0.26152.2415-0.06780.1719-0.1603-0.26970.0015-0.44040.07580.21070.0664-0.1024-0.0040.0689-0.16480.01120.125518.6835-1.863521.7525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 156
2X-RAY DIFFRACTION2{ B|* }B1 - 156

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