[English] 日本語
Yorodumi
- PDB-8pfa: X-ray structure of the Thermus thermophilus K167R mutant of the P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pfa
TitleX-ray structure of the Thermus thermophilus K167R mutant of the PilF-GSPIIB domain in the c-di-GMP bound state
Componentsc-di-GMP binding domain of the ATPase enzyme PilF
KeywordsMOTOR PROTEIN / PilT class / GSPII / ligand binding / c-di-GMP
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type II secretion system protein GspE, N-terminal / MshEN domain / Type II secretion system protein GspE, N-terminal superfamily / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / Chem-C2E / ATP-binding motif-containing protein pilF
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNeissner, K. / Woehnert, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)Wo 901/12-1 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The structural basis for high-affinity c-di-GMP binding to the GSPII-B domain of the traffic ATPase PilF from Thermus thermophilus.
Authors: Neissner, K. / Keller, H. / Kirchner, L. / Dusterhus, S. / Duchardt-Ferner, E. / Averhoff, B. / Wohnert, J.
History
DepositionJun 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: c-di-GMP binding domain of the ATPase enzyme PilF
B: c-di-GMP binding domain of the ATPase enzyme PilF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,23219
Polymers32,5952
Non-polymers2,63717
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-132 kcal/mol
Surface area14490 Å2
Unit cell
Length a, b, c (Å)108.165, 108.165, 87.446
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

-
Components

#1: Protein c-di-GMP binding domain of the ATPase enzyme PilF / c-di-GMP binding domain of the ATPase enzyme PilF


Mass: 16297.575 Da / Num. of mol.: 2 / Mutation: K167R
Source method: isolated from a genetically manipulated source
Details: c-di-GMP binding domain of the ATPase enzyme PilF / Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: pilF, TT_C1622 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72H73
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.5 M LiSO4 0.1 M NaAcetate pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→39.62 Å / Num. obs: 35354 / % possible obs: 99.94 % / Redundancy: 10.3 % / Biso Wilson estimate: 43.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05805 / Rpim(I) all: 0.01905 / Rrim(I) all: 0.06116 / Net I/σ(I): 18.04
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 1.393 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3588 / CC1/2: 0.737 / Rpim(I) all: 0.4531

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.62 Å / SU ML: 0.2264 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.0521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 1774 5.02 %
Rwork0.1893 33575 -
obs0.191 35349 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 162 96 2363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712313
X-RAY DIFFRACTIONf_angle_d1.25233161
X-RAY DIFFRACTIONf_chiral_restr0.0621350
X-RAY DIFFRACTIONf_plane_restr0.0055387
X-RAY DIFFRACTIONf_dihedral_angle_d44.0807311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.34671380.32542574X-RAY DIFFRACTION100
1.85-1.90.32111380.27452608X-RAY DIFFRACTION99.96
1.9-1.960.30031370.24842571X-RAY DIFFRACTION100
1.96-2.030.25821350.23522602X-RAY DIFFRACTION100
2.03-2.120.24011330.22622541X-RAY DIFFRACTION100
2.12-2.210.27461380.21692601X-RAY DIFFRACTION99.93
2.21-2.330.2431330.21112569X-RAY DIFFRACTION99.96
2.33-2.470.24861400.20982597X-RAY DIFFRACTION100
2.48-2.670.2811330.21862596X-RAY DIFFRACTION100
2.67-2.930.2541390.22092572X-RAY DIFFRACTION100
2.93-3.360.27341380.21092582X-RAY DIFFRACTION100
3.36-4.230.19931350.17312582X-RAY DIFFRACTION100
4.23-39.620.17651370.15272580X-RAY DIFFRACTION99.52
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)
12.66458401018-0.4055903598550.05610360322667.048853094160.9902425668911.626588838610.0399005109090.0476091684551-0.0168563590957-0.158562091460.04802775972560.01864597712520.07219945184120.13041956025-0.08466761863890.251970123137-0.0279267769566-0.02289579950540.353538135683-0.0351923677040.257798289829-9.886-16.53322.15
26.37117926695-1.674407269751.126375974673.00855790668-0.02966554536081.12939156169-0.0489575145411-0.0414321083529-0.0789221082560.1241440284130.02817302706160.07181745371180.0895074800588-0.05491960443330.001934128483350.416544881372-0.0936856901827-0.05453858355760.4111706502390.03747854571660.328970395989-34.681-29.04621.318
34.730019816482.10567308514-0.4518556199954.06277425385-0.03749046389882.05200966350.213724700888-0.3858254851490.131070764760.500194956826-0.0639513137882-0.114375196665-0.0560397472128-0.2966316502830.1006575160491.017788707820.131896471961-0.04791998488131.202378007570.05158302255370.906959744126-25.092-26.09126.375
40.08273731049790.0433966769581-0.3075842363710.6409014193820.2658388132461.63204010281-0.4371875915640.6377105339940.3381567249320.2267986695630.342513120660.08247708076020.01088180757090.0562233327070.06608078133090.9351002439920.0332905257360.0699388960860.753092174199-0.08059902705540.830020782026-28.558-17.43522.993
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 9:146 OR RESID 201:201 ) )A9 - 146
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 9:146 OR RESID 201:201 ) )A201
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 9:145 OR RESID 201:201 ) )B9 - 145
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 9:145 OR RESID 201:201 ) )B201
5X-RAY DIFFRACTION3( CHAIN A AND RESID 202:204 ) OR ( CHAIN B AND RESID 202:208 )A202 - 204
6X-RAY DIFFRACTION3( CHAIN A AND RESID 202:204 ) OR ( CHAIN B AND RESID 202:208 )B202 - 208
7X-RAY DIFFRACTION4( CHAIN A AND RESID 205:207 ) OR ( CHAIN B AND RESID 209:210 )A205 - 207
8X-RAY DIFFRACTION4( CHAIN A AND RESID 205:207 ) OR ( CHAIN B AND RESID 209:210 )B209 - 210

+
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