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- PDB-7r5p: Strep-tag FtrA-P19 from Rubrivivax gelatinosus in complex with co... -

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Basic information

Entry
Database: PDB / ID: 7r5p
TitleStrep-tag FtrA-P19 from Rubrivivax gelatinosus in complex with copper and iron
ComponentsFtrA-P19 protein
KeywordsTRANSPORT PROTEIN / Copper binding / iron transport
Function / homologyCOPPER (I) ION
Function and homology information
Biological speciesRubrivivax gelatinosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 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 11, 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
C: FtrA-P19 protein
D: FtrA-P19 protein
E: FtrA-P19 protein
F: FtrA-P19 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,74119
Polymers129,1526
Non-polymers58913
Water7,170398
1
A: FtrA-P19 protein
B: FtrA-P19 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2887
Polymers43,0512
Non-polymers2385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-71 kcal/mol
Surface area14090 Å2
MethodPISA
2
C: FtrA-P19 protein
D: FtrA-P19 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2266
Polymers43,0512
Non-polymers1764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-75 kcal/mol
Surface area13820 Å2
MethodPISA
3
E: FtrA-P19 protein
F: FtrA-P19 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2266
Polymers43,0512
Non-polymers1764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-72 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.575, 77.996, 115.225
Angle α, β, γ (deg.)90.000, 95.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FtrA-P19 protein


Mass: 21525.312 Da / Num. of mol.: 6
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-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 25% PEG4K, 0.1 M Tris-HCl, 0.2 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: 0.980115 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980115 Å / Relative weight: 1
ReflectionResolution: 1.68→49 Å / Num. obs: 92927 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.4
Reflection shellResolution: 1.68→1.86 Å / Rmerge(I) obs: 0.738 / Num. unique obs: 4342 / CC1/2: 0.725

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Processing

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

7r3p


Resolution: 1.68→32.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3373 4.97 %RANDOM
Rwork0.179 ---
obs0.181 67876 71 %-
Displacement parametersBiso max: 132.9 Å2 / Biso mean: 32.94 Å2 / Biso min: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.3848 Å20 Å2-1.4298 Å2
2--1.1729 Å20 Å2
3----3.5577 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 1.68→32.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 16 398 7776
Biso mean--37.16 33.73 -
Num. residues----933
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2489SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1295HARMONIC5
X-RAY DIFFRACTIONt_it7695HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion959SEMIHARMONIC5
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_contact8820SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7695HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10488HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion17.75
LS refinement shellResolution: 1.68→1.8 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2957 68 5.01 %
Rwork0.2614 1290 -
all0.2631 1358 -
obs--7.74 %
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)
10.97410.09520.11371.24640.42053.52270.03050.2606-0.0025-0.3548-0.0455-0.1136-0.2369-0.12040.0150.05480.09290.03240.1306-0.0158-0.040212.99980.374322.0232
21.00520.1059-0.40291.22340.85674.5940.03-0.2884-0.10110.3107-0.1380.00550.0044-0.49740.10790.01210.064-0.03260.1540.0069-0.09149.273-0.406847.9733
31.5009-0.0251-0.03280.7788-0.4524.6681-0.11850.18120.2186-0.1720.12390.1213-0.06360.2332-0.00550.06570.0085-0.0881-0.10960.0137-0.036226.9414-16.6499-6.4746
41.70220.7507-0.00082.4169-0.64613.28190.1327-0.44870.03160.3483-0.03020.08210.20280.0842-0.10250.11540.06620.0023-0.0143-0.0578-0.063825.2621-25.556217.9814
51.9936-0.5053-0.5631.248-0.28575.5327-0.0354-0.362-0.08570.1116-0.0664-0.0398-0.22340.17360.1019-0.02650.0292-0.0230.03570.0031-0.06892.600530.356854.1762
62.3218-0.3481-0.53911.7368-0.61035.1250.2740.55620.0052-0.3956-0.23380.0998-0.1593-0.4524-0.04020.03930.1573-0.03760.1412-0.0521-0.1078-1.746831.44828.7389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 156
2X-RAY DIFFRACTION2{ B|* }B1 - 156
3X-RAY DIFFRACTION3{ E|* }E1 - 156
4X-RAY DIFFRACTION4{ F|* }F1 - 155
5X-RAY DIFFRACTION5{ D|* }D1 - 156
6X-RAY DIFFRACTION6{ C|* }C2 - 155

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