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- PDB-2o5p: Crystal structure of the full length ferric pyoverdine outer memb... -

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Basic information

Entry
Database: PDB / ID: 2o5p
TitleCrystal structure of the full length ferric pyoverdine outer membrane receptor FpvA of Pseudomonas aeruginosa in its apo form
ComponentsFerripyoverdine receptor
KeywordsTRANSPORT PROTEIN / FpvA / pyoverdine / pseudomonas / cobessi
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 (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / 3-Layer(bab) Sandwich / 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: 2.77 Å
AuthorsCobessi, D.
CitationJournal: Structure / Year: 2007
Title: A beta strand lock exchange for signal transduction in TonB-dependent transducers on the basis of a common structural motif.
Authors: Brillet, K. / Journet, L. / Celia, H. / Paulus, L. / Stahl, A. / Pattus, F. / Cobessi, D.
History
DepositionDec 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,41213
Polymers173,1122
Non-polymers1,30011
Water00
1
A: Ferripyoverdine receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4768
Polymers86,5561
Non-polymers9207
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Unit cell
Length a, b, c (Å)189.880, 128.780, 139.150
Angle α, β, γ (deg.)90.00, 130.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 136 - 815 / Label seq-ID: 93 - 772

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is one FpvA molecule and the asymmetric unit contains 2 FpvA molecules.

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Components

#1: Protein Ferripyoverdine receptor


Mass: 86556.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fpvA / Plasmid: ppvr2 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: P48632
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#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.: 1 / Source method: obtained synthetically / Formula: C18H38O6 / Comment: C8E5, detergent*YM

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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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 1.3-1.4 M Na2HPO4, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97565 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97565 Å / Relative weight: 1
ReflectionResolution: 2.77→30.47 Å / Num. obs: 63018 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.93 % / Rsym value: 8 / Net I/σ(I): 13.7
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 2.67 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 7865 / Rsym value: 39.1 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2iah

2iah


Resolution: 2.77→30.47 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.891 / SU B: 25.664 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.62 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24724 3195 5.1 %RANDOM
Rwork0.2077 ---
obs0.20976 59777 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.538 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å21.44 Å2
2---0.17 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.77→30.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12110 0 74 0 12184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212476
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.93916947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95851523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69424.263638
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.414151962
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7451578
X-RAY DIFFRACTIONr_chiral_restr0.0960.21762
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029780
X-RAY DIFFRACTIONr_nbd_refined0.2220.25167
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28340
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2545
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.25
X-RAY DIFFRACTIONr_mcbond_it0.4581.57708
X-RAY DIFFRACTIONr_mcangle_it0.798212136
X-RAY DIFFRACTIONr_scbond_it1.25835522
X-RAY DIFFRACTIONr_scangle_it2.0584.54811
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5425 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.420.5
medium thermal0.52
LS refinement shellResolution: 2.772→2.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 184 -
Rwork0.299 3225 -
obs--72.22 %
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)
12.5738-0.0582-0.22232.8689-0.87881.4513-0.14510.440.2592-0.34390.052-0.01940.0969-0.21560.09310.0071-0.1073-0.0156-0.04930.0303-0.0222-58.22-15.4710.361
21.54440.7434-0.34261.6215-0.35491.2468-0.10090.30410.1384-0.1792-0.0102-0.01030.0992-0.20390.1111-0.0171-0.0753-0.0039-0.06690.01450.0302-59.863-21.8115.173
310.16572.3843-3.94648.9959-0.69238.8463-0.3173-0.43520.03990.07270.34480.404-0.0102-0.0537-0.02750.07970.04990.03440.17040.10340.1233-29.354.44-9.922
41.2244-0.2391-0.22291.9671-0.65452.5232-0.0028-0.07930.03620.05230.1230.0243-0.04350.1865-0.1202-0.116-0.02760.0616-0.2318-0.0263-0.1697-6.687-5.96137.737
50.75230.1415-0.25371.4312-0.63671.70180.0296-0.03480.02620.10050.11920.0116-0.14150.109-0.1489-0.0801-0.03750.0566-0.1727-0.0446-0.1181-4.7860.51533.178
62.3812-0.2227-1.16535.7761-2.16226.8539-0.0004-0.0748-0.14160.126-0.02910.35110.5060.06550.02940.02440.09590.0437-0.12580.0383-0.0571-10.004-30.70852.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BB139 - 27696 - 233
2X-RAY DIFFRACTION2BB277 - 815234 - 772
3X-RAY DIFFRACTION3BB44 - 1171 - 74
4X-RAY DIFFRACTION4AA139 - 27696 - 233
5X-RAY DIFFRACTION5AA277 - 815234 - 772
6X-RAY DIFFRACTION6AA44 - 1381 - 95

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