[English] 日本語
Yorodumi
- PDB-5zfq: Crystal structure of PilT-4, a retraction ATPase motor of Type IV... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zfq
TitleCrystal structure of PilT-4, a retraction ATPase motor of Type IV pilus , from Geobacter sulfurreducens
ComponentsTwitching motility pilus retraction protein
KeywordsTRANSPORT PROTEIN / Type IV pilus / retraction ATPase / PilT-4
Function / homology
Function and homology information


Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold ...Pilus retraction protein PilT/PilU / Beta-Lactamase - #90 / Bacterial type II secretion system protein E signature. / Type II/IV secretion system protein / Type II/IV secretion system protein / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Twitching motility pilus retraction protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsThakur, K.G. / Kapoor, S. / Solanki, V.
Funding support India, 2items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research India
Department of Biotechnology India
CitationJournal: FEBS J. / Year: 2018
Title: Structural insights into the mechanism of Type IVa pilus extension and retraction ATPase motors
Authors: Solanki, V. / Kapoor, S. / Thakur, K.G.
History
DepositionMar 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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: Twitching motility pilus retraction protein
B: Twitching motility pilus retraction protein


Theoretical massNumber of molelcules
Total (without water)87,1902
Polymers87,1902
Non-polymers00
Water2,414134
1
A: Twitching motility pilus retraction protein
B: Twitching motility pilus retraction protein

A: Twitching motility pilus retraction protein
B: Twitching motility pilus retraction protein

A: Twitching motility pilus retraction protein
B: Twitching motility pilus retraction protein


Theoretical massNumber of molelcules
Total (without water)261,5706
Polymers261,5706
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21790 Å2
ΔGint-10 kcal/mol
Surface area85160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.760, 181.760, 123.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-466-

HOH

-
Components

#1: Protein Twitching motility pilus retraction protein


Mass: 43595.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Strain: PCA / Gene: pilT-4, GSU1492 / Plasmid: pET-Duet
Details (production host): TEV cleavable 6xHistidine tag and Kanamycin resistance marker
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q74D27
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.0M succinic acid pH7.0 / PH range: 7.0-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→97.198 Å / Num. obs: 23914 / % possible obs: 99.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 42.32 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.042 / Rrim(I) all: 0.11 / Rsym value: 0.101 / Net I/av σ(I): 6.9 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.6-2.746.10.6231.234390.2670.680.62398.6
2.74-2.916.30.4281.832610.180.4650.42898.8
2.91-3.116.40.2942.630750.1220.320.29499.1
3.11-3.366.40.1754.328880.0730.190.17599.8
3.36-3.686.60.1136.526890.0470.1230.113100
3.68-4.116.60.0798.724160.0330.0860.079100
4.11-4.756.60.05312.521680.0220.0580.05399.8
4.75-5.816.60.0561118100.0230.0610.05699.6
5.81-8.226.60.05510.714130.0220.060.05599
8.22-22.726.40.02720.77550.0110.0290.02794

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å37.61 Å
Translation3.5 Å37.61 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.22data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.24data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JVU

3jvu


Resolution: 2.6→22.72 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.98
RfactorNum. reflection% reflection
Rfree0.2436 1227 5.15 %
Rwork0.1905 --
obs0.1934 23805 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.47 Å2 / Biso mean: 45.3822 Å2 / Biso min: 25.95 Å2
Refinement stepCycle: final / Resolution: 2.6→22.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 0 134 5766
Biso mean---39.04 -
Num. residues----720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015735
X-RAY DIFFRACTIONf_angle_d1.2347772
X-RAY DIFFRACTIONf_chiral_restr0.044917
X-RAY DIFFRACTIONf_plane_restr0.0061010
X-RAY DIFFRACTIONf_dihedral_angle_d15.9082190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.7040.35271440.27122459260398
2.704-2.82680.32571540.25472453260798
2.8268-2.97550.33541370.24842478261598
2.9755-3.16150.34341190.25272513263299
3.1615-3.40490.31361290.21092516264599
3.4049-3.74610.27911390.1962524266399
3.7461-4.2850.18471380.16092500263899
4.285-5.38680.17341200.14812564268499
5.3868-22.72090.19481470.16172571271898
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)
12.4797-0.3185-1.04682.8159-0.30523-0.0950.0703-0.0546-0.21260.0351-0.0550.1310.06070.00040.32950.0042-0.01950.3655-0.05020.297630.818384.722432.8909
20.64960.2874-0.23071.22160.04252.1619-0.0852-0.0513-0.061-0.02310.1464-0.0720.13160.327200.29430.01720.01330.36560.0040.438215.052269.559150.6163
30.9668-0.8643-0.06780.5722-0.05231.2687-0.14180.18390.42030.20180.0375-0.1603-0.1373-0.20530.00060.3534-0.0304-0.04120.35760.02710.48562.090278.587751.5593
40.4264-0.3564-0.2960.50280.50040.2582-0.0774-0.30810.1550.00470.06980.1383-0.20930.2623-0.00050.3797-0.03490.02460.3986-0.07590.43569.345181.516963.274
51.72520.98310.6682.6134-0.11511.23780.1427-0.7576-0.10270.3355-0.20220.17190.2315-0.006-0.00040.3869-0.0718-0.02610.5034-0.04560.33612.473276.637769.2156
60.8725-0.67230.27250.9186-0.56311.72540.1989-0.6665-0.3210.219-0.1747-0.26970.282-0.2483-0.00240.48950.0114-0.06150.59690.05660.508828.469774.401373.9636
72.6123-0.024-0.09863.0458-0.77792.2046-0.03050.1783-0.1484-0.2446-0.0421-0.07340.12690.02970.00020.3647-0.00790.01470.3612-0.05160.30932.9275121.374132.9206
80.40.3964-0.42022.37190.1481.90160.0172-0.07050.02980.01560.0207-0.0861-0.06490.23740.00020.31880.0327-0.01920.3795-0.02520.369836.093298.785349.9696
91.182-0.4782-0.58761.16660.84320.7784-0.08910.05550.04630.25830.01340.53040.0022-0.0392-00.4229-0.01470.01490.3617-0.03430.480525.270798.443761.8963
101.5549-0.31230.51751.19711.14431.33770.2081-0.44280.04530.7396-0.2987-0.13390.18720.35310.00060.6464-0.009-0.05960.3714-0.00080.370833.8262103.821471.5098
110.23060.0135-0.34470.03420.04930.13290.2669-0.2586-0.06260.4717-0.194-0.65840.64920.35520.00360.6735-0.0207-0.08550.42840.02170.495642.6393108.258673.1188
120.40980.13150.18710.74560.18640.5759-0.263-0.26590.1280.31080.07890.0569-0.28860.0465-00.4837-0.0522-0.0520.5012-0.0390.383639.1178119.422574.7475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 100 )A-6 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 185 )A101 - 185
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 221 )A186 - 221
4X-RAY DIFFRACTION4chain 'A' and (resid 222 through 246 )A222 - 246
5X-RAY DIFFRACTION5chain 'A' and (resid 247 through 308 )A247 - 308
6X-RAY DIFFRACTION6chain 'A' and (resid 309 through 353 )A309 - 353
7X-RAY DIFFRACTION7chain 'B' and (resid -6 through 100 )B-6 - 100
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 199 )B101 - 199
9X-RAY DIFFRACTION9chain 'B' and (resid 200 through 271 )B200 - 271
10X-RAY DIFFRACTION10chain 'B' and (resid 272 through 308 )B272 - 308
11X-RAY DIFFRACTION11chain 'B' and (resid 309 through 328 )B309 - 328
12X-RAY DIFFRACTION12chain 'B' and (resid 329 through 353 )B329 - 353

+
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://pdbjlc1.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