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- PDB-6r44: Structure of the SBP FpvC in complex with Ni2+ ion from P.aerugin... -

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Basic information

Entry
Database: PDB / ID: 6r44
TitleStructure of the SBP FpvC in complex with Ni2+ ion from P.aeruginosa from P21 space group
ComponentsProbable adhesion protein
KeywordsTRANSPORT PROTEIN / Solute binding protein / transport system
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
NICKEL (II) ION / Probable adhesion protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMorera, S. / Marty, L.
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 21, 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 / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7974
Polymers64,6802
Non-polymers1172
Water4,450247
1
A: Probable adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3982
Polymers32,3401
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3982
Polymers32,3401
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.920, 41.380, 104.620
Angle α, β, γ (deg.)90.00, 95.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable adhesion protein


Mass: 32339.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA2407 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I174
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 16% PEG 6K, 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: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.99→43.19 Å / Num. obs: 38967 / % possible obs: 99.1 % / Redundancy: 5.8 % / Biso Wilson estimate: 34.45 Å2 / Rsym value: 0.161 / Net I/σ(I): 6.13
Reflection shellResolution: 1.99→2.05 Å / Num. unique obs: 8580 / Rsym value: 1.071

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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: 1.99→43.19 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.153 / SU Rfree Cruickshank DPI: 0.153
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1949 5 %RANDOM
Rwork0.195 ---
obs0.197 38967 99.1 %-
Displacement parametersBiso mean: 41.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.3102 Å20 Å21.5206 Å2
2---1.5183 Å20 Å2
3---3.8285 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.99→43.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4181 0 2 247 4430
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014272HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15803HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1481SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes724HARMONIC5
X-RAY DIFFRACTIONt_it4272HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion19.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion577SEMIHARMONIC5
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_contact5092SEMIHARMONIC4
LS refinement shellResolution: 2→2.01 Å
RfactorNum. reflection% reflection
Rfree0.45 -5 %
Rwork0.32 741 -
obs--76.63 %
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)
10.8434-0.12640.13810.8117-0.1041.8576-0.04790.0761-0.0053-0.00540.08330.0196-0.01490.2774-0.0354-0.0966-0.0033-0.0077-0.11390.0079-0.042217.8279-17.707311.3376
21.5053-0.02830.45030.8129-0.17532.0115-0.03260.17590.0141-0.00410.0378-0.0866-0.00550.4052-0.0052-0.0159-0.0138-0.0343-0.0475-0.004-0.084445.99060.259163.4344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|41 - A|131 A|142 - A|320 }
2X-RAY DIFFRACTION2{ B|41 - B|131 B|142 - B|320 }

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