[English] 日本語
Yorodumi
- PDB-5lt9: Ligand binding domain of Pseudomonas aeruginosa PAO1 amino acid c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lt9
TitleLigand binding domain of Pseudomonas aeruginosa PAO1 amino acid chemoreceptors PctB in complex with L-Arg
ComponentsMethyl-accepting chemotaxis protein PctB
KeywordsSIGNALING PROTEIN / Ligand binding domain / CHEMOTACTIC TRANSDUCER
Function / homology
Function and homology information


amino acid binding / response to amino acid / chemotaxis / signal transduction / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / Periplasmic sensor-like domain superfamily / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
ARGININE / HAMP domain-containing protein / Methyl-accepting chemotaxis protein PctB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGavira, J.A. / Rico-Jimenez, M. / Ortega, A. / Conejero-Muriel, M. / Zhulin, I. / Krell, T.
Funding support Spain, 1items
OrganizationGrant numberCountry
MICINNBIO2013-4297-P Spain
Citation
Journal: Mbio / Year: 2020
Title: How Bacterial Chemoreceptors Evolve Novel Ligand Specificities
Authors: Gavira, J.A. / Jimenez-Rico, M. / Pineda-Molina, E. / Krell, T.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2013
Title: Purification, crystallization and preliminary crystallographic analysis of the ligand-binding regions of the PctA and PctB chemoreceptors from Pseudomonas aeruginosa in complex with amino acids.
Authors: Rico-Jimenez, M. / Munoz-Martinez, F. / Krell, T. / Gavira, J.A. / Pineda-Molina, E.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Dec 12, 2018Group: Data collection / Structure summary / Category: audit_author / struct / Item: _struct.title
Revision 1.4Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.5Apr 29, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.6Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein PctB
B: Methyl-accepting chemotaxis protein PctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1116
Polymers63,6452
Non-polymers4664
Water905
1
A: Methyl-accepting chemotaxis protein PctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0213
Polymers31,8231
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyl-accepting chemotaxis protein PctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0903
Polymers31,8231
Non-polymers2672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.729, 111.729, 117.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Methyl-accepting chemotaxis protein PctB


Mass: 31822.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pctB_2, AOY09_01347 / Plasmid: PET28B PLUS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6UK01, UniProt: Q9HW91*PLUS
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.02 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 7.5
Details: Capillary counterdiffusion: 1.25 M sodium citrate & 0.1 M Hepes pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→117.55 Å / Num. obs: 17440 / % possible obs: 100 % / Redundancy: 9 % / Biso Wilson estimate: 86.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.04 / Rrim(I) all: 0.122 / Net I/σ(I): 12.9 / Num. measured all: 157570 / Scaling rejects: 3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3-3.186.60.9370.6921100
9-117.558.10.0470.998199.8

-
Processing

Software
NameVersionClassification
Aimless0.2.14data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T65

5t65


Resolution: 3→37.353 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.27
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 879 5.06 %Random
Rwork0.2147 ---
obs0.2164 17385 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 197.05 Å2 / Biso mean: 86.1166 Å2 / Biso min: 34.88 Å2
Refinement stepCycle: final / Resolution: 3→37.353 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 43 5 3791
Biso mean--84.57 76.87 -
Num. residues----487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033926
X-RAY DIFFRACTIONf_angle_d0.6385348
X-RAY DIFFRACTIONf_chiral_restr0.04599
X-RAY DIFFRACTIONf_plane_restr0.005702
X-RAY DIFFRACTIONf_dihedral_angle_d14.2352352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0004-3.18830.33251440.340727152859100
3.1883-3.43430.31611530.281526972850100
3.4343-3.77960.29141470.247527292876100
3.7796-4.32580.25791390.202227312870100
4.3258-5.44730.22421520.175827592911100
5.4473-37.35620.20861440.19962875301999
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)
16.83361.82284.67562.1084-0.35084.5296-0.661-0.39320.97380.0002-0.53720.028-0.1640.1521.20560.42580.03940.1040.8055-0.02090.5885-11.157240.104835.5474
22.25511.14022.96676.85171.79168.4219-0.36280.18560.1306-0.4519-0.5010.16090.7346-0.47550.86820.54030.00830.14330.5967-0.00860.5281-19.339835.24812.5923
33.8416-1.12590.21232.967-1.29887.3195-0.19370.094-0.3497-0.7455-0.0753-0.46011.47950.54720.36490.72670.04430.22080.4923-0.02240.7442-11.846324.768917.369
46.80.89615.53214.88444.56538.49190.0752-0.0292-0.3333-0.2220.0774-0.35020.23440.2252-0.0960.4562-0.00780.24950.43140.07360.5448-14.167131.336723.3361
53.69140.6073.81789.3216-1.098.6512-0.0564-0.0085-0.5122-0.15910.0088-1.08770.28030.96360.12760.5070.0890.21850.72270.09370.67922.899631.756735.3927
64.62232.44083.8372.42361.46763.44740.7975-1.8191-0.81320.3014-0.6938-0.1881.02280.0076-0.06210.8425-0.0350.11061.31620.16431.27674.244826.624746.9876
75.8254.90853.35134.69530.85927.22850.4295-0.2118-1.10810.4646-0.1943-0.68710.34250.834-0.07150.44070.08570.11980.76790.09440.72983.725736.025943.8838
85.40283.40154.33544.59723.34648.7537-0.3682-0.0770.89160.73390.7749-0.36920.02171.6314-0.68580.42260.0333-0.04470.7689-0.14540.6679-18.274661.995929.2053
92.0928-0.32620.70788.0277-0.38884.9114-0.03220.2931-0.1356-0.63160.12950.30250.0907-0.2709-0.17390.3754-0.03890.00750.79050.01110.4694-32.609253.456510.87
101.65891.0765-0.21117.1465.27273.8784-0.0305-0.05790.44590.1957-0.20510.3466-0.30950.07390.08120.49560.0126-0.03720.77010.01120.6135-29.738568.55928.5094
115.6712-0.74450.96962.9172.457.1465-0.1625-0.7590.8872-0.83550.5089-0.3981-0.5909-0.3203-0.47380.7853-0.0609-0.01160.7968-0.17780.934-24.242182.092232.9716
124.6552-0.75011.44899.48414.08825.0980.052-0.67060.28770.45981.2067-1.0956-0.94011.2322-0.46960.44470.0248-0.05320.7855-0.08030.7767-21.270473.052836.1161
138.5503-1.9421-0.11952.7225-4.17439.33671.52321.0738-0.91480.9904-0.18560.89141.8559-0.271-1.18790.96050.0512-0.10430.8676-0.08420.6446-9.809181.768263.7917
142.51840.18660.28041.3491-3.0066.8989-0.5728-0.18830.7982-2.3945-0.48631.4822-0.8706-0.321.11491.1251-0.46560.16890.1367-1.10340.6575-9.846427.463614.0372
150.20550.4833-0.13911.1075-0.33880.1006-0.0279-0.10340.34440.09740.1873-0.2667-0.03860.31050.34280.29010.1912-0.09051.1479-0.07660.5348-38.476355.975714.3734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 77 )A39 - 77
2X-RAY DIFFRACTION2chain 'A' and (resid 78 through 104 )A78 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 152 )A105 - 152
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 183 )A153 - 183
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 219 )A184 - 219
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 231 )A220 - 231
7X-RAY DIFFRACTION7chain 'A' and (resid 232 through 272 )A232 - 272
8X-RAY DIFFRACTION8chain 'B' and (resid 40 through 74 )B40 - 74
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 167 )B75 - 167
10X-RAY DIFFRACTION10chain 'B' and (resid 168 through 219 )B168 - 219
11X-RAY DIFFRACTION11chain 'B' and (resid 220 through 247 )B220 - 247
12X-RAY DIFFRACTION12chain 'B' and (resid 248 through 273 )B248 - 273
13X-RAY DIFFRACTION13chain 'B' and (resid 274 through 292 )B274 - 292
14X-RAY DIFFRACTION14chain 'A' and (resid 301 through 301 )A301
15X-RAY DIFFRACTION15chain 'B' and (resid 301 through 301 )B301

+
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