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- PDB-6ru4: Structure of the SBP FpvC from pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 6ru4
TitleStructure of the SBP FpvC from pseudomonas aeruginosa in complex with Mn2+
ComponentsProbable adhesion protein
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


metal 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 / Probable adhesion protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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
DepositionMay 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: Probable adhesion protein
B: Probable adhesion protein
C: Probable adhesion protein
D: Probable adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,70541
Polymers122,5204
Non-polymers2,18537
Water3,585199
1
A: Probable adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,56316
Polymers30,6301
Non-polymers93415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0989
Polymers30,6301
Non-polymers4688
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,12410
Polymers30,6301
Non-polymers4949
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Probable adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9196
Polymers30,6301
Non-polymers2895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.010, 178.290, 66.820
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Probable adhesion protein


Mass: 30629.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA2407
Variant: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Production host: Escherichia coli (E. coli) / References: UniProt: Q9I174
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MPEG 2K, 0.1 M 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 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.49→44.57 Å / Num. obs: 35191 / % possible obs: 98.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 71.47 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.07 / Rsym value: 0.17 / Net I/σ(I): 8.58
Reflection shellResolution: 2.49→2.64 Å / Num. unique obs: 5188

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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: 2.49→44.57 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU R Cruickshank DPI: 1.689 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.929 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.294
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1760 5.01 %RANDOM
Rwork0.196 ---
obs0.198 35152 98.3 %-
Displacement parametersBiso mean: 64.04 Å2
Baniso -1Baniso -2Baniso -3
1--2.515 Å20 Å2-6.48 Å2
2--0.5194 Å20 Å2
3---1.9956 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.49→44.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8324 0 70 199 8593
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018534HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1611569HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2952SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1441HARMONIC5
X-RAY DIFFRACTIONt_it8534HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion19.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1146SEMIHARMONIC5
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_contact9564SEMIHARMONIC4
LS refinement shellResolution: 2.49→2.52 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.393 -5.26 %
Rwork0.3146 667 -
all0.3187 704 -
obs--53.16 %
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)
10.56060.3527-0.15843.5482-1.65011.64950.0327-0.0761-0.04160.0743-0.1411-0.1527-0.12590.07450.1084-0.26070.0542-0.0142-0.31140.0115-0.437761.36378.961123.9827
22.337-1.2669-1.40765.08511.55791.77750.20030.09490.0726-0.2135-0.07020.0052-0.30350.0935-0.1302-0.3056-0.0350.1117-0.4455-0.0302-0.502240.837111.133-8.5806
31.0258-0.562-0.2924.2365-1.12881.24240.16010.0392-0.05550.1453-0.1873-0.081-0.02690.06660.0272-0.3235-0.0474-0.0824-0.33280.0335-0.480539.3757-32.158135.8441
41.4755-1.2845-0.39143.22930.46831.84550.0970.1206-0.0843-0.1875-0.14550.03380.1243-0.15970.0485-0.29270.0046-0.0861-0.3487-0.019-0.529463.1395-29.96791.0783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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