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- PDB-6r5s: Structure of the SBP FpvC from pseudomonas aeruginosa in complex ... -

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Basic information

Entry
Database: PDB / ID: 6r5s
TitleStructure of the SBP FpvC from pseudomonas aeruginosa in complex with Fe(II)
ComponentsAdhesion protein
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


zinc ion transport / 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
: / Adhesion protein / High-affinity zinc uptake system protein ZnuA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 25, 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 1.2Sep 25, 2019Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code ..._entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3Jan 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 1.4Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesion protein
B: Adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2285
Polymers65,0552
Non-polymers1743
Water59433
1
A: Adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5832
Polymers32,5271
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adhesion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6453
Polymers32,5271
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.010, 44.190, 179.760
Angle α, β, γ (deg.)90.00, 95.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Adhesion protein


Mass: 32527.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: psaA, C0044_17990, CAZ10_34375, DZ962_30765, NCTC13719_02701, PAMH19_5875
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069PX18, UniProt: Q9I174*PLUS
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 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: 1.738 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.738 Å / Relative weight: 1
ReflectionResolution: 2.75→37.62 Å / Num. obs: 14604 / % possible obs: 96.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 71.61 Å2 / Rsym value: 0.01 / Net I/σ(I): 9.35
Reflection shellResolution: 2.75→2.91 Å / Num. unique obs: 4343

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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: 2.75→37.62 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.353
RfactorNum. reflection% reflectionSelection details
Rfree0.242 731 5.01 %RANDOM
Rwork0.189 ---
obs0.192 14601 96.7 %-
Displacement parametersBiso mean: 57 Å2
Baniso -1Baniso -2Baniso -3
1--2.1297 Å20 Å20.491 Å2
2---0.9148 Å20 Å2
3---3.0446 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.75→37.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 6 33 4234
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014304HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.175844HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1489SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes728HARMONIC5
X-RAY DIFFRACTIONt_it4304HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion20.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion578SEMIHARMONIC5
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_contact4817SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.77 Å / Total num. of bins used: 36
RfactorNum. reflection% reflection
Rfree0.2333 -5.17 %
Rwork0.2603 385 -
all0.2588 406 -
obs--88.5 %
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)
12.2073-0.07550.03681.7903-0.23234.40580.029-0.45970.01420.25410.1256-0.055-0.0055-0.2398-0.1546-0.38380.0819-0.0421-0.39230.0175-0.347812.621318.58220.5456
22.73430.3418-0.16052.3117-0.54424.7475-0.08420.6866-0.0017-0.24370.21110.02160.1368-0.4666-0.1269-0.404-0.10280.0755-0.29730.0189-0.34214.83964.249968.9233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|42 - A|131 A|142 - A|322 }
2X-RAY DIFFRACTION2{ B|42 - B|131 B|142 - B|321 }

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