[English] 日本語
Yorodumi
- PDB-5it5: Thermus thermophilus PilB core ATPase region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5it5
TitleThermus thermophilus PilB core ATPase region
ComponentsATP binding motif-containing protein PilF
KeywordsTRANSPORT PROTEIN / ATPase / AAA+ / hexamer / Type IV pilus
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / Type II secretion system protein GspE, N-terminal / MshEN domain / Beta-Lactamase - #90 / 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 / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases ...: / Type II secretion system protein GspE, N-terminal / MshEN domain / Beta-Lactamase - #90 / 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 / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ADENOSINE-5'-TRIPHOSPHATE / Type IV pilus assembly ATPase PilB / ATP binding motif-containing protein PilF
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.648 Å
AuthorsMancl, J. / Robinson, H. / Black, W. / Yang, Z. / Schubot, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1417726 United States
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of a Type IV Pilus Assembly ATPase: Insights into the Molecular Mechanism of PilB from Thermus thermophilus.
Authors: Mancl, J.M. / Black, W.P. / Robinson, H. / Yang, Z. / Schubot, F.D.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: ATP binding motif-containing protein PilF
A: ATP binding motif-containing protein PilF
B: ATP binding motif-containing protein PilF
E: ATP binding motif-containing protein PilF
C: ATP binding motif-containing protein PilF
D: ATP binding motif-containing protein PilF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)258,72620
Polymers255,1626
Non-polymers3,56414
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23760 Å2
ΔGint-80 kcal/mol
Surface area93410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.550, 133.560, 208.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

-
Protein , 1 types, 6 molecules FABECD

#1: Protein
ATP binding motif-containing protein PilF


Mass: 42526.992 Da / Num. of mol.: 6 / Fragment: unp residues 180-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: pilF
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8VRL1, UniProt: Q5SLC9*PLUS

-
Non-polymers , 5 types, 383 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Magnesium chloride, bis-tris, PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.276396 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.276396 Å / Relative weight: 1
ReflectionResolution: 2.648→65.29 Å / Num. obs: 87967 / % possible obs: 99.95 % / Redundancy: 2 % / Rmerge(I) obs: 0.1243 / Net I/σ(I): 5.83
Reflection shellResolution: 2.65→2.74 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P9R

1p9r


Resolution: 2.648→65.289 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 2838 3.23 %
Rwork0.2083 85024 -
obs0.2104 87862 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.4 Å2 / Biso mean: 41.9005 Å2 / Biso min: 16.64 Å2
Refinement stepCycle: final / Resolution: 2.648→65.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17903 0 194 369 18466
Biso mean--39.06 39.2 -
Num. residues----2310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01118353
X-RAY DIFFRACTIONf_angle_d1.35424821
X-RAY DIFFRACTIONf_chiral_restr0.0492890
X-RAY DIFFRACTIONf_plane_restr0.0063198
X-RAY DIFFRACTIONf_dihedral_angle_d17.1047053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.648-2.69370.3951430.33954192433599
2.6937-2.74260.38381460.331641684314100
2.7426-2.79540.35761430.316141874330100
2.7954-2.85250.35961260.299642504376100
2.8525-2.91450.3241690.280441784347100
2.9145-2.98230.34311470.265941984345100
2.9823-3.05690.30971390.254642134352100
3.0569-3.13950.35051380.254142064344100
3.1395-3.23190.3561390.257842204359100
3.2319-3.33620.27771400.24642534393100
3.3362-3.45540.28461380.223842114349100
3.4554-3.59380.25461390.205742554394100
3.5938-3.75730.25851400.191642234363100
3.7573-3.95540.23951380.18542694407100
3.9554-4.20320.28531400.17542584398100
4.2032-4.52760.2291410.157142684409100
4.5276-4.98310.19751410.145942964437100
4.9831-5.70380.22381420.171543124454100
5.7038-7.18480.25381430.191343584501100
7.1848-65.30890.19761460.14424509465599

+
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