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- PDB-6r6k: Structure of a FpvC mutant from pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6r6k
TitleStructure of a FpvC mutant from pseudomonas aeruginosa
ComponentsABC transporter substrate-binding protein
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


zinc ion transport / cell adhesion / metal ion binding
Similarity search - Function
Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / : / High-affinity zinc uptake system protein ZnuA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMorera, S. / Vigouroux, A.
CitationJournal: Febs J. / Year: 2020
Title: A unique ferrous iron binding mode is associated with large conformational changes for the transport protein FpvC of Pseudomonas aeruginosa.
Authors: Vigouroux, A. / Aumont-Nicaise, M. / Boussac, A. / Marty, L. / Lo Bello, L. / Legrand, P. / Brillet, K. / Schalk, I.J. / Morera, S.
History
DepositionMar 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,08139
Polymers63,6482
Non-polymers2,43237
Water3,171176
1
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,19437
Polymers31,8241
Non-polymers2,37036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-0 kcal/mol
Surface area13030 Å2
MethodPISA
2
B: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8862
Polymers31,8241
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint2 kcal/mol
Surface area13310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.270, 53.560, 84.390
Angle α, β, γ (deg.)90.00, 93.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ABC transporter substrate-binding protein


Mass: 31824.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: D8668_16520 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G3N2S3, UniProt: Q9I174*PLUS

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Non-polymers , 5 types, 213 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPG 2K, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→43.74 Å / Num. obs: 40831 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 43.59 Å2 / Rpim(I) all: 0.061 / Rsym value: 0.106 / Net I/σ(I): 9.12
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 6474

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R3Z

6r3z


Resolution: 2.1→43.74 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.9 / SU R Cruickshank DPI: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.31 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.225
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1396 5.04 %RANDOM
Rwork0.194 ---
obs0.196 27703 67.8 %-
Displacement parametersBiso mean: 86.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.0573 Å20 Å2-1.595 Å2
2--2.5204 Å20 Å2
3---4.5369 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.1→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4146 0 155 176 4477
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014340HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.135821HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1514SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes719HARMONIC5
X-RAY DIFFRACTIONt_it4340HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion18.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion568SEMIHARMONIC5
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_contact4982SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.202 -3.42 %
Rwork0.198 536 -
all0.1981 555 -
obs--19.22 %
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)
15.8474-0.2816-0.07621.38980.16990.79760.17050.36480.29970.0387-0.11740.0279-0.07970.107-0.053-0.40960.0081-0.0346-0.3990.0133-0.3287-22.4023-14.131539.4837
212.348-2.06330.25022.03660.54635.45130.94755.4853-0.5739-0.2697-1.27890.17760.3701-0.73540.3314-0.94520.5007-0.07532.0611-0.3255-1.1598-33.2532-19.337410.6918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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