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- PDB-7r3p: Apoform of the periplasmic FtrA/P19 protein from Rubrivivax gelat... -

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Basic information

Entry
Database: PDB / ID: 7r3p
TitleApoform of the periplasmic FtrA/P19 protein from Rubrivivax gelatinosus (His-tag)
ComponentsFtrA-P19 protein
KeywordsTRANSPORT PROTEIN / COPPER BINDING / IRON TRANSPORT
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesRubrivivax gelatinosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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)39,5308
Polymers38,9482
Non-polymers5826
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-71 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.160, 80.300, 82.740
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: 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)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 400 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 2 M AS, 0.1 M citrate sodium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→48.12 Å / Num. obs: 78363 / % possible obs: 99.7 % / Redundancy: 13 % / Biso Wilson estimate: 21.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.9
Reflection shellResolution: 1.4→1.48 Å / Num. unique obs: 12299 / CC1/2: 0.718

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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: 3LZL

3lzl


Resolution: 1.4→48.12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.054
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3919 5 %RANDOM
Rwork0.179 ---
obs0.18 78363 99.7 %-
Displacement parametersBiso max: 112.96 Å2 / Biso mean: 26.52 Å2 / Biso min: 13.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.9282 Å20 Å20 Å2
2---1.5104 Å20 Å2
3---0.5822 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: final / Resolution: 1.4→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2478 0 33 400 2911
Biso mean--44.14 39.63 -
Num. residues----314
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d889SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes459HARMONIC5
X-RAY DIFFRACTIONt_it2694HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion338SEMIHARMONIC5
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_contact3385SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2694HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3685HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion4.81
X-RAY DIFFRACTIONt_other_torsion15.63
LS refinement shellResolution: 1.4→1.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3463 78 4.97 %
Rwork0.3042 1490 -
all0.3064 1568 -
obs--88.66 %
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)
10.67940.1889-0.19940.4683-0.11120.55490.0051-0.0076-0.08080.0083-0.00420.01810.0322-0.0071-0.0009-0.04510.0035-0.0096-0.032-0.0002-0.02330.1493-26.3914-3.5813
20.6698-0.15070.07560.7412-0.3910.86650.03820.15560.0879-0.1225-0.0948-0.0531-0.07560.05740.05650.1120.00820.00410.12890.01860.099313.9042-10.0132-18.0789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 157
2X-RAY DIFFRACTION2{ B|* }B1 - 157

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