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- PDB-6r3z: Structure of the SBP FpvC in complex with Ni2+ ion from P. aerugi... -

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Basic information

Entry
Database: PDB / ID: 6r3z
TitleStructure of the SBP FpvC in complex with Ni2+ ion from P. aeruginosa in P212121 space group
ComponentsProbable adhesion protein
KeywordsTRANSPORT PROTEIN / solute binding protein (transport system)
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
NICKEL (II) ION / High-affinity zinc uptake system protein ZnuA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 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 / 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 1.3May 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8339
Polymers32,3401
Non-polymers4938
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint18 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.570, 62.690, 90.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Probable adhesion protein


Mass: 32339.770 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 1.91 Å3/Da / Density % sol: 35.66 %
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 1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.65→39.26 Å / Num. obs: 30063 / % possible obs: 97.8 % / Redundancy: 10 % / Biso Wilson estimate: 27.93 Å2 / Rpim(I) all: 0.051 / Rsym value: 0.11 / Net I/σ(I): 12.8
Reflection shellResolution: 1.65→1.75 Å / Num. unique obs: 4251

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: model soved by SAD

Resolution: 1.65→39.26 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1504 5 %RANDOM
Rwork0.184 ---
obs0.186 30063 98 %-
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-9.1488 Å20 Å20 Å2
2---9.192 Å20 Å2
3---0.0432 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.65→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 29 255 2349
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012138HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972888HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d742SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes358HARMONIC5
X-RAY DIFFRACTIONt_it2138HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.23
X-RAY DIFFRACTIONt_other_torsion15.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion284SEMIHARMONIC5
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_contact2669SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.66 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.4255 -4.98 %
Rwork0.3199 572 -
all0.3244 602 -
obs--76.43 %
Refinement TLS params.Method: refined / Origin x: -17.5627 Å / Origin y: -2.3093 Å / Origin z: 11.0395 Å
111213212223313233
T-0.0142 Å20.005 Å2-0.0055 Å2-0.0116 Å20.0128 Å2---0.0183 Å2
L0.5679 °20.0627 °2-0.0503 °2-0.7999 °2-0.2322 °2--0.344 °2
S0.0075 Å °-0.0105 Å °0.0016 Å °-0.0562 Å °0 Å °-0.023 Å °0.0413 Å °0.02 Å °-0.0075 Å °
Refinement TLS groupSelection details: { A|41 - A|130 A|142 - A|316 }

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