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- PDB-2w78: Structures of P. aeruginosa FpvA bound to heterologous pyoverdine... -

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Basic information

Entry
Database: PDB / ID: 2w78
TitleStructures of P. aeruginosa FpvA bound to heterologous pyoverdines: FpvA-Pvd(ATCC13535)-Fe complex
Components
  • FERRIPYOVERDINE RECEPTOR
  • SER-LYS-GLY-FHO-LYS-FH7-SER
KeywordsRECEPTOR / FPVA / IRON / MEMBRANE / TONB BOX / TRANSPORT / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / IRON TRANSPORT / CELL OUTER MEMBRANE / TONB-DEPENDENT TRANSPORTER
Function / homology
Function and homology information


pyoverdine biosynthetic process / siderophore-iron import into cell / 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, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site ...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, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / Maltoporin; Chain A / 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 / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / 3-Layer(bab) Sandwich / Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Chem-PVE / Ferripyoverdine receptor
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jun 27, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.5Jul 10, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Jul 31, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.8Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_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 "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" 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 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERRIPYOVERDINE RECEPTOR
B: FERRIPYOVERDINE RECEPTOR
C: SER-LYS-GLY-FHO-LYS-FH7-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,01917
Polymers173,9363
Non-polymers2,08314
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
C: SER-LYS-GLY-FHO-LYS-FH7-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1928
Polymers87,3802
Non-polymers8126
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-43.9 kcal/mol
Surface area32120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.556, 130.937, 139.367
Angle α, β, γ (deg.)90.00, 130.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#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: Protein/peptide SER-LYS-GLY-FHO-LYS-FH7-SER


Mass: 823.892 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 14 molecules

#3: 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
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PVE / (1S)-1-CARBOXY-5-[(3-CARBOXYPROPANOYL)AMINO]-8,9-DIHYDROXY-1,2,3,4-TETRAHYDROPYRIMIDO[1,2-A]QUINOLIN-11-IUM


Mass: 376.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N3O7
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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Details

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: 3.86 Å3/Da / Density % sol: 67.88 % / 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: X11 / Wavelength: 0.817
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.817 Å / Relative weight: 1
ReflectionResolution: 3→107 Å / Num. obs: 50836 / % possible obs: 96.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O5P

2o5p


Resolution: 3→97.59 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 30.657 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2583 5.1 %RANDOM
Rwork0.191 ---
obs0.194 48251 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å22.17 Å2
2---0.47 Å20 Å2
3---2.2 Å2
Refinement stepCycle: LAST / Resolution: 3→97.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12164 0 125 0 12289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02212608
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.94517096
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.02751529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14824.263638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.219151971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6551578
X-RAY DIFFRACTIONr_chiral_restr0.1250.21769
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029829
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.25186
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.28354
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2445
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3050.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7691.57759
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.327212190
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.08335691
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3154.54906
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: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 192
Rwork0.29 3594
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)
11.8291-0.83390.53265.9872-0.60955.97710.07470.0113-0.08970.0515-0.07510.34340.48170.10110.0003-0.10760.04080.042-0.13750.0431-0.1245-10.706-31.81353.541
20.4580.1317-0.24340.914-0.39871.03230.0062-0.02930.00460.00220.0864-0.0042-0.07740.0668-0.0925-0.1239-0.04150.037-0.1328-0.0407-0.1289-5.059-0.96134.703
38.11752.0807-1.75128.90650.38049.245-0.2772-0.42350.1274-0.11840.34980.21540.0270.0325-0.0727-0.150.06610.0733-0.06990.1224-0.0437-29.9134.465-10.031
41.26130.5436-0.3031.0278-0.26360.7609-0.0960.24690.0791-0.07550.0240.0012-0.0242-0.13490.072-0.1083-0.0466-0.0066-0.0884-0.0016-0.0395-60.333-20.68714.365
51.7796-0.29310.06914.9499-1.15030.26730.03230.01190.01140.12550.02010.01950.0256-0.0871-0.0523-0.0098-0.00920.00710.0004-0.0029-0.0213-65.969-38.08420.849
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
5X-RAY DIFFRACTION5C1 - 9

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