[English] 日本語
Yorodumi
- PDB-1xkh: Pyoverdine outer membrane receptor FpvA from Pseudomonas aerugino... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xkh
TitlePyoverdine outer membrane receptor FpvA from Pseudomonas aeruginosa PAO1 bound to pyoverdine
Components
  • Ferripyoverdine receptor
  • Pyoverdin C-E
KeywordsMEMBRANE PROTEIN / PYOVERDINE / FPVA / TONB BOX / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / TONB DEPENDENT RECEPTOR
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
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 ...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 / Beta Complex / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PYOVERDIN C-E CHROMOPHORE / Chem-PVE / : / Ferripyoverdine receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsCobessi, D. / Celia, H. / Folschweiller, N. / Schalk, I.J. / Abdallah, M.A. / Pattus, F.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: The Crystal Structure of the Pyoverdine Outer Membrane Receptor FpvA from Pseudomonas aeruginosa at 3.6A Resolution
Authors: Cobessi, D. / Celia, H. / Folschweiller, N. / Schalk, I.J. / Abdallah, M.A. / Pattus, F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray analysis of the outer membrane pyoverdine receptor FpvA from Pseudomonas aeruginosa
Authors: Cobessi, D. / Celia, H. / Folschweiller, N. / Heymann, M. / Schalk, I.J. / Abdallah, M.A. / Pattus, F.
History
DepositionSep 29, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Structure summary / Version format compliance
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Apr 22, 2015Group: Structure summary
Revision 1.6Apr 3, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ferripyoverdine receptor
B: Ferripyoverdine receptor
C: Ferripyoverdine receptor
I: Pyoverdin C-E
J: Pyoverdin C-E
K: Pyoverdin C-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,45612
Polymers237,0386
Non-polymers1,4176
Water00
1
A: Ferripyoverdine receptor
I: Pyoverdin C-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4854
Polymers79,0132
Non-polymers4722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferripyoverdine receptor
J: Pyoverdin C-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4854
Polymers79,0132
Non-polymers4722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ferripyoverdine receptor
K: Pyoverdin C-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4854
Polymers79,0132
Non-polymers4722
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.451, 231.342, 121.695
Angle α, β, γ (deg.)90.00, 104.57, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Ferripyoverdine receptor / Pyoverdine outer membrane receptor / Selenomethionine substituted protein


Mass: 78015.758 Da / Num. of mol.: 3 / Fragment: residues 129-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fpva / Plasmid: PVR2 / Production host: Pseudomonas aeruginosa (bacteria) / Strain (production host): PAO503 / References: UniProt: P48632
#2: Protein/peptide Pyoverdin C-E


Type: Polypeptide / Class: Metal transport / Mass: 997.062 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS ...Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
Source: (synth.) Pseudomonas aeruginosa (bacteria) / References: NOR: NOR00190, PYOVERDIN C-E CHROMOPHORE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PVE / (1S)-1-CARBOXY-5-[(3-CARBOXYPROPANOYL)AMINO]-8,9-DIHYDROXY-1,2,3,4-TETRAHYDROPYRIMIDO[1,2-A]QUINOLIN-11-IUM


Type: Polypeptide / Class: Metal transport / Mass: 376.341 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H18N3O7
Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS ...Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
References: PYOVERDIN C-E CHROMOPHORE
Compound detailsPYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS ...PYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS SPECIES. PYOVERDINE IS NECESSARY FOR INFECTION IN SEVERAL DIFFERENT DISEASE MODELS. THE OCCURRENCE OF PYOVERDINE-DEFECTIVE STRAINS IN CHRONIC INFECTIONS OF PATIENTS WITH CYSTIC FIBROSIS AND THE EXTREMELY HIGH SEQUENCE DIVERSITY OF GENES INVOLVED IN PYOVERDINE SYNTHESIS AND UPTAKE INDICATE THAT PYOVERDINE PRODUCTION IS SUBJECT TO HIGH EVOLUTIONARY PRESSURE. PYOVERDINE-DEPENDENT IRON TRANSPORT IS ALSO CRUCIAL FOR BIOFILM DEVELOPMENT, FURTHER EXPANDING THE IMPORTANCE OF THESE SIDEROPHORES IN PSEUDOMONAS BIOLOGY. HERE, PYOVERDINE-CHROMOPHORE COMPLEX IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE OF CHAIN I (SEQRES) AND THE LIGAND (HET) PVE1I.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 13-16% PEG 4000, 20-25% ethylene glycol as cryoprectant in a 0.1M sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979413, 0.979632, 0.977801
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 3, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794131
20.9796321
30.9778011
ReflectionResolution: 3.6→20 Å / Num. all: 41896 / Num. obs: 41896 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Rsym value: 0.129 / Net I/σ(I): 8.46
Reflection shellResolution: 3.6→3.7 Å / Mean I/σ(I) obs: 1.14 / Rsym value: 0.375 / % possible all: 96

-
Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ferrichrome outer membrane receptor FhuA from Escherichia coli.

Resolution: 3.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 2090 RANDOM
Rwork0.259 --
all-41885 -
obs-41885 -
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.54 Å
Luzzati d res low-10 Å
Luzzati sigma a0.57 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16626 0 93 0 16719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00996
X-RAY DIFFRACTIONc_angle_deg1.55855
LS refinement shellResolution: 3.6→3.73 Å
RfactorNum. reflection
Rfree0.41 187
Rwork0.4016 -
obs-3870

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more