[English] 日本語
Yorodumi
- PDB-7prq: Structure of the ligand binding domain of the PctD (PA4633) chemo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7prq
TitleStructure of the ligand binding domain of the PctD (PA4633) chemoreceptor of Pseudomonas aeruginosa PAO1 in complex with choline.
ComponentsProbable chemotaxis transducer
KeywordsSIGNALING PROTEIN / Ligand binding domain / Pseudomonas aeruginosa / chemotactic transducer
Function / homology
Function and homology information


chemotaxis / membrane => GO:0016020 / signal transduction
Similarity search - Function
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
CHOLINE ION / Probable chemotaxis transducer
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGavira, J.A. / Matilla, M.A. / Martin-Mora, D. / Krell, T.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-74875-P Spain
Spanish Ministry of Economy and CompetitivenessBio2016-76779-P Spain
CitationJournal: Mbio / Year: 2022
Title: Chemotaxis of the Human Pathogen Pseudomonas aeruginosa to the Neurotransmitter Acetylcholine.
Authors: Matilla, M.A. / Velando, F. / Tajuelo, A. / Martin-Mora, D. / Xu, W. / Sourjik, V. / Gavira, J.A. / Krell, T.
History
DepositionSep 22, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable chemotaxis transducer
B: Probable chemotaxis transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,68412
Polymers76,9062
Non-polymers77710
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint18 kcal/mol
Surface area25330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.138, 104.864, 118.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Probable chemotaxis transducer


Mass: 38453.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ligand binding domain
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4633 / Plasmid: PET28B+
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9HVF8
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H14NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.54 %
Crystal growTemperature: 293 K / Method: counter-diffusion
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% w/v Polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→118.6 Å / Num. obs: 48037 / % possible obs: 99.8 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.055 / Rrim(I) all: 0.117 / Net I/σ(I): 10 / Num. measured all: 214721 / Scaling rejects: 105
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.054.41.0434730.6170.5631.18799.7
8.94-118.63.80.0296290.9990.0160.03399.4

-
Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RaptorX

Resolution: 2→78.56 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.956
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2165 2390 4.98 %
Rwork0.1754 45559 -
obs0.1775 47949 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.95 Å2
Refinement stepCycle: LAST / Resolution: 2→78.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 51 312 5139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01275176
X-RAY DIFFRACTIONf_angle_d1.25687052
X-RAY DIFFRACTIONf_chiral_restr0.0615758
X-RAY DIFFRACTIONf_plane_restr0.0108954
X-RAY DIFFRACTIONf_dihedral_angle_d6.6769753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.31441610.30132583X-RAY DIFFRACTION99.53
2.04-2.090.31281330.2512677X-RAY DIFFRACTION99.75
2.09-2.130.28851280.21812643X-RAY DIFFRACTION100
2.13-2.190.23421240.20012655X-RAY DIFFRACTION99.86
2.19-2.250.24111350.19012665X-RAY DIFFRACTION99.82
2.25-2.310.25931390.18692648X-RAY DIFFRACTION99.64
2.31-2.390.23051320.18192642X-RAY DIFFRACTION99.5
2.39-2.470.25321380.17482675X-RAY DIFFRACTION99.96
2.47-2.570.2151220.17242683X-RAY DIFFRACTION99.82
2.57-2.690.25581430.16922675X-RAY DIFFRACTION99.82
2.69-2.830.20421590.16562652X-RAY DIFFRACTION99.93
2.83-3.010.21451380.16982655X-RAY DIFFRACTION99.5
3.01-3.240.24891380.17412696X-RAY DIFFRACTION99.86
3.24-3.570.19271490.15652687X-RAY DIFFRACTION99.72
3.57-4.080.18511280.15222747X-RAY DIFFRACTION99.65
4.08-5.140.17651560.13992733X-RAY DIFFRACTION99.52
5.14-78.560.21391670.20992843X-RAY DIFFRACTION98.98
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)
15.960907339845.84572232792.392598376346.53661546082.384060590831.52619637772-0.003559740124080.0364585153642-0.3148388848350.04843206945680.143336993934-0.5135545098270.01789504716530.159544224688-0.1553736936930.1993501213240.0584797015436-0.01805903877880.222555543795-0.01779158926690.211225749471-17.84926673276.6210031283122.9445356543
21.387989844490.723488155564-0.00432077137313.13380672062-1.333835833391.72108071075-0.02591239059880.0318376978872-0.0284463428533-0.2277569190160.04579261437360.1242644620520.219359733891-0.130397457896-0.04574247238610.2655716266360.00581812958609-0.03597398933320.225951319857-0.006793142037340.196970714834-40.196008364-6.9323688924314.3090412436
32.412944686411.318904245520.5546656087553.17664924143-0.1797954760272.97525585498-0.1943741005640.350600456262-0.00432627840078-0.7692395123930.2320787526610.2189145807970.12199253744-0.122190590531-0.03525349728860.404538094424-0.0330203366288-0.04380706371590.2684881467050.005296668683120.182004198792-38.3668236713-6.344746977942.00946441508
43.127455803252.763539796190.6069541473113.571836787740.6646507196341.4090320467-0.2083674276040.391451903265-0.0826388282178-0.3846930236320.196270576945-0.2369679194840.1204176167920.1516916985850.01341500323210.2305244872730.05289743009210.02653767256930.2814975822370.008715439292460.18257613346-22.36264387852.320197801028.18930379925
54.29603673639-0.715685528803-0.1091020974712.026356061451.865093951646.79287811616-0.2665679889591.163699010520.241396032917-1.056771905040.462896870574-0.83112411736-0.6178017273580.865972829582-0.2003378584480.366500286426-0.09991264693940.05298224311570.5913084102410.0001122470973120.439310548355-12.476307022713.56810619984.22805916478
65.070365015210.4282198344631.883119290842.038561217981.591970358636.61800190427-0.09828702008651.10839245299-0.447334225163-0.4559248811280.0689052772116-1.169891313030.485575997710.9051723107720.05688104713530.498409480790.1512184532810.1015162513210.658501091731-0.07286676771880.679490590659-0.16289914132212.145938456713.6858769364
74.053926745253.240890131251.488305499386.668063657841.556388947743.103448357430.03700846379210.490732845356-0.2667777498250.04111913304480.236133494576-1.026601563130.1012890727190.383547806059-0.2916509815350.2423065773410.0959741448101-0.01120229142520.327854410533-0.0178038830880.447136439192-5.3967953700216.722897190719.9348677712
87.79443213434.97001060552.332149272483.956504821441.457347420621.205835226920.196552409608-0.1133034386760.3826007124270.380916159857-0.2018323250840.0462262418336-0.002970458872140.1047029476940.03514527756790.255412649090.0172312736227-0.03275925773750.204077698967-0.005724579019870.224489276095-17.491136830314.670623344232.3806344485
95.308925209392.06350533036-0.02426970849623.422636174220.5267847747952.968023123130.06252785637670.0209560833958-0.07082500525660.135681651448-0.134398551440.3378399239970.271252790092-0.2549300918950.04318447284370.2248200033830.0005215680978520.01149712348330.155296366052-0.02929926754830.197143611893-44.0460122079-10.08820983830.5864845795
102.794428861541.349709849151.349655470962.663340060740.427790769115.862960359770.0326782775442-0.466831784580.2069012979970.41312733915-0.1155958204040.315611489777-0.311654681448-0.4005171248180.07425536936450.3038299165570.003261719402460.05853627923690.24813557623-0.05104828564130.232202287331-39.53633545942.7244913081939.7117982301
113.459379716861.212020263710.641822525392.212078753640.456290652280.7919587790680.161692675519-0.3287645901420.1639979606610.559787510291-0.160430501141-0.229751593210.008984320470780.0248624816897-0.00600719737780.4076351278040.00580589081225-0.03189951373510.2732612528380.0110483685570.255931129771-21.89809638038.3485981277743.0257752271
126.981789064851.814882605461.808113879993.157359377230.3297605637912.873886303980.401062458674-0.451323289407-0.06738572879910.662951195497-0.321566834415-0.6306790401810.04648457099610.405081833055-0.04054110887710.420264461101-0.00865099164835-0.1381939372590.2832867702370.003251586287420.342052433075-10.233512989918.809037840442.5516942483
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 67 )AA25 - 671 - 43
22chain 'A' and (resid 68 through 102 )AA68 - 10244 - 78
33chain 'A' and (resid 103 through 152 )AA103 - 15279 - 128
44chain 'A' and (resid 153 through 241 )AA153 - 241129 - 217
55chain 'A' and (resid 242 through 266 )AA242 - 266218 - 242
66chain 'A' and (resid 267 through 290 )AA267 - 290243 - 266
77chain 'A' and (resid 291 through 328 )AA291 - 328267 - 304
88chain 'B' and (resid 17 through 67 )BF17 - 671 - 51
99chain 'B' and (resid 68 through 152 )BF68 - 15252 - 136
1010chain 'B' and (resid 153 through 205 )BF153 - 205137 - 189
1111chain 'B' and (resid 206 through 280 )BF206 - 280190 - 264
1212chain 'B' and (resid 281 through 332 )BF281 - 332265 - 316

+
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://pdbjlvh1.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