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- PDB-2w75: Structures of P. aeruginosa FpvA bound to heterologous pyoverdine... -

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Basic information

Entry
Database: PDB / ID: 2w75
TitleStructures of P. aeruginosa FpvA bound to heterologous pyoverdines: Apo-FpvA
ComponentsFERRIPYOVERDINE RECEPTOR
KeywordsRECEPTOR / TONB BOX / TRANSPORT / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / IRON TRANSPORT / TONB-DEPENDENT TRANSPORTER
Function / homology
Function and homology information


pyoverdine biosynthetic process / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane
Similarity search - Function
Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor ...Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, plug domain / Maltoporin; Chain A / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / 3-Layer(bab) Sandwich / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ferripyoverdine receptor
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGreenwald, J. / Nader, M. / Celia, H. / Gruffaz, C. / Meyer, J.-M. / Schalk, I.J. / Pattus, F.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Fpva Bound to Non-Cognate Pyoverdines: Molecular Basis of Siderophore Recognition by an Iron Transporter.
Authors: Greenwald, J. / Nader, M. / Celia, H. / Gruffaz, C. / Geoffroy, V. / Meyer, J.M. / Schalk, I.J. / Pattus, F.
History
DepositionDec 20, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FERRIPYOVERDINE RECEPTOR
B: FERRIPYOVERDINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,76314
Polymers173,1122
Non-polymers1,65112
Water00
1
A: FERRIPYOVERDINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8279
Polymers86,5561
Non-polymers1,2718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FERRIPYOVERDINE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9365
Polymers86,5561
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)193.794, 129.526, 140.952
Angle α, β, γ (deg.)90.00, 130.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein FERRIPYOVERDINE RECEPTOR / FPVA


Mass: 86556.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PPVR2 / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / Strain (production host): K691 / References: UniProt: P48632
#2: Chemical ChemComp-N8E / 3,6,9,12,15-PENTAOXATRICOSAN-1-OL / N-OCTYLPENTAOXYETHYLENE / PENTAETHYLENE GLYCOL MONOOCTYL ETHER / OCTYLPENTAGLYCOL N-OCTYLPENTAOXYETHYLENE


Mass: 350.491 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O6 / Comment: C8E5, detergent*YM
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
Sequence detailsSIGNAL PEPTIDE (RESIDUES 1-43) IS NOT IN THE CRYSTALLIZED PROTEIN

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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: 3.92 Å3/Da / Density % sol: 68.41 % / Description: NONE
Crystal growDetails: 1.3M NAH2PO4, 0.1M MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.9→107 Å / Num. obs: 53997 / % possible obs: 92.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 1.9
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.9 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.4.0054refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O5P

2o5p


Resolution: 2.9→107.21 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.859 / SU B: 29.438 / SU ML: 0.26 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 1.475 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2742 5.1 %RANDOM
Rwork0.212 ---
obs0.214 51255 92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.32 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å23.75 Å2
2---1.76 Å20 Å2
3---3.2 Å2
Refinement stepCycle: LAST / Resolution: 2.9→107.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12108 0 98 0 12206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02212522
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.94216991
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.17651523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11424.263638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.612151962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7291578
X-RAY DIFFRACTIONr_chiral_restr0.1260.21762
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6661.57550
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.303212136
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17834972
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6524.54855
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 193
Rwork0.29 3802
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)
12.3548-1.13840.7517.591-1.08456.74620.11560.0391-0.14660.0868-0.10840.43220.6170.0322-0.0072-0.15440.04530.0389-0.10.045-0.1372-10.7061-31.812753.5412
20.72040.1132-0.25831.3086-0.5241.4056-0.0152-0.02970.01230.01460.1111-0.0025-0.10160.082-0.0958-0.1754-0.06790.0252-0.1708-0.0614-0.1883-5.0591-0.961334.7035
39.12861.5986-2.77939.9172-0.127210.2104-0.2628-0.50480.1274-0.00910.25080.45810.08130.16490.012-0.10990.06080.03230.04650.11870.0385-29.91264.465-10.031
41.55120.5191-0.35981.2067-0.17791.0348-0.0740.2830.1087-0.14110.01080.0099-0.0894-0.15540.0631-0.0897-0.0544-0.0264-0.09520.0145-0.0315-60.3334-20.687314.3645
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 129
2X-RAY DIFFRACTION2A130 - 815
3X-RAY DIFFRACTION3B44 - 117
4X-RAY DIFFRACTION4B136 - 815

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