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- PDB-5fok: Crystal structure of the siderophore receptor PiuA from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 5fok
TitleCrystal structure of the siderophore receptor PiuA from Pseudomonas aeruginosa
ComponentsIRON TRANSPORT OUTER MEMBRANE RECEPTOR
KeywordsMETAL TRANSPORT / TONB-DEPENDENT RECEPTOR / SIDEROPHORE RECEPTOR / OUTER-MEMBRANE PROTEIN
Function / homology
Function and homology information


siderophore transport / siderophore uptake transmembrane transporter activity / porin activity / pore complex / cell outer membrane / iron ion transport / signaling receptor activity
Similarity search - Function
TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / 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 / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / 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 / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Probable TonB-dependent siderophore receptor PiuA
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoynie, L. / Naismith, J.H.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structure and Function of the PiuA and PirA Siderophore-Drug Receptors from Pseudomonas aeruginosa and Acinetobacter baumannii.
Authors: Moynie, L. / Luscher, A. / Rolo, D. / Pletzer, D. / Tortajada, A. / Weingart, H. / Braun, Y. / Page, M.G. / Naismith, J.H. / Kohler, T.
History
DepositionNov 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 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: IRON TRANSPORT OUTER MEMBRANE RECEPTOR
B: IRON TRANSPORT OUTER MEMBRANE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,53915
Polymers160,8262
Non-polymers2,71313
Water10,719595
1
A: IRON TRANSPORT OUTER MEMBRANE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1609
Polymers80,4131
Non-polymers1,7478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: IRON TRANSPORT OUTER MEMBRANE RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3786
Polymers80,4131
Non-polymers9655
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)194.010, 132.970, 73.590
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1727-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 27 - 720 / Label seq-ID: 28 - 721

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.978, 0.0522, 0.202), (0.0547, -0.9985, -0.0066), (0.2013, 0.0175, -0.9794)
Vector: -1.925, 21.523, 19.6746)

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Components

#1: Protein IRON TRANSPORT OUTER MEMBRANE RECEPTOR


Mass: 80412.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: G3XCY8
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.89 Å3/Da / Density % sol: 57.44 % / Description: NONE
Crystal growpH: 8.5
Details: 32% PEG 400, 0.05 M TRIS PH 8.5, 0.05 M SODIUM SULPHATE AND 0.05 M LICL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→71.93 Å / Num. obs: 142771 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
XDSdata reduction
xia2data scaling
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FCP

2fcp


Resolution: 1.9→71.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.251 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21058 7162 5 %RANDOM
Rwork0.18843 ---
obs0.18955 135518 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.477 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20.48 Å2
2---0.16 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.9→71.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10231 0 163 595 10989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0210675
X-RAY DIFFRACTIONr_bond_other_d0.0020.029789
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.94514459
X-RAY DIFFRACTIONr_angle_other_deg0.65322490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37451317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26723.973521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.181151661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2941575
X-RAY DIFFRACTIONr_chiral_restr0.080.21565
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212280
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022599
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 36935 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 554 -
Rwork0.237 9934 -
obs--99.7 %
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)
11.31630.02670.37510.33340.30944.94870.05150.02010.04820.0245-0.041-0.0949-0.07050.1185-0.01060.05780.0122-0.06870.06710.01740.159525.695-234.932
22.1242-0.52730.20040.7343-0.27620.51360.0302-0.0832-0.0960.0661-0.03440.03380.10160.03730.00420.09790.0335-0.05380.0372-0.02850.089934.927-20.058-5.748
31.082-0.38370.09920.4272-0.3390.85240.04920.08970.0545-0.0024-0.0709-0.08570.10460.11670.02180.0540.0306-0.04370.0287-0.010.061329.319-5.1491.006
41.1145-2.45491.940223.0882-14.38219.1640.3248-0.09820.0673-0.17520.13420.90920.2548-0.0982-0.45890.30790.0437-0.00250.1021-0.0170.143336.2698.6819.456
53.87746.0944-1.206811.3299-1.95311.80810.3589-0.43820.18310.29-0.33630.4216-0.2625-0.1204-0.02270.1942-0.0076-0.0540.20540.0130.133828.127-17.46923.524
62.4402-0.1910.84361.76561.50634.6545-0.0324-0.09130.01140.00130.0305-0.12550.04420.0820.00180.05180.0012-0.04230.07090.07290.128417.395-23.42412.898
70.9038-0.8082-0.74082.54411.26411.50480.0165-0.0013-0.15720.10870.0638-0.08710.24270.0293-0.08030.08980.0141-0.08620.0384-0.00750.134814.21-18.266-3.077
815.0406-3.2546-14.19972.1462.903613.45130.4621-0.65130.4282-0.1144-0.0862-0.2389-0.55080.6568-0.37590.3464-0.0733-0.13210.13450.02430.216427.74654.12519.107
91.25850.8409-0.79171.06860.76364.7261-0.0540.0032-0.08740.1093-0.0790.05030.3685-0.05320.1330.1213-0.0244-0.06250.0983-0.01450.197119.48842.54720.699
102.45050.55990.14051.4362-0.00621.1208-0.02230.05290.0882-0.0102-0.01020.0128-0.08880.08970.03250.1135-0.0236-0.06720.0222-0.00720.082227.85343.62832.472
111.00580.4765-0.21470.5874-0.24010.632-0.0021-0.067-0.01210.0103-0.0185-0.00590.0021-0.01010.02060.0843-0.0137-0.03180.0237-0.02140.059125.86729.04725.23
120.87874.7337-3.0525.7813-16.560910.7013-0.00460.08370.1104-0.21830.35280.75210.1714-0.2337-0.34820.3271-0.02050.05830.0757-0.05560.272335.09214.85217.239
133.5864-4.64390.50287.8042-1.4841.4480.09860.3171-0.0451-0.1512-0.15920.24110.04-0.12610.06050.1409-0.086-0.0780.12590.05060.154625.38744.4373.745
140.77060.58860.27971.38130.08131.1985-0.03750.02870.16620.01380.08520.0341-0.1135-0.021-0.04770.048-0.0134-0.04130.0688-0.01240.198710.24441.93121.97
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 101
2X-RAY DIFFRACTION2A102 - 239
3X-RAY DIFFRACTION3A240 - 445
4X-RAY DIFFRACTION4A446 - 470
5X-RAY DIFFRACTION5A471 - 530
6X-RAY DIFFRACTION6A531 - 601
7X-RAY DIFFRACTION7A602 - 720
8X-RAY DIFFRACTION8B27 - 43
9X-RAY DIFFRACTION9B44 - 101
10X-RAY DIFFRACTION10B102 - 219
11X-RAY DIFFRACTION11B220 - 445
12X-RAY DIFFRACTION12B446 - 470
13X-RAY DIFFRACTION13B471 - 542
14X-RAY DIFFRACTION14B543 - 720

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