[English] 日本語
Yorodumi
- PDB-5g23: Type IV-like pilin TTHA1219 from Thermus thermophilus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5g23
TitleType IV-like pilin TTHA1219 from Thermus thermophilus
ComponentsTYPE-IV LIKE PILIN TTHA1219
KeywordsSTRUCTURAL PROTEIN / NATURAL COMPETENCE / TYPE IV PILUS / DNA UPTAKE
Function / homologyProkaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation site / cell outer membrane / Probable general secretion pathway protein J
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.85 Å
AuthorsKaruppiah, V. / Derrick, J.P.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structures of Type Iv Pilins from Thermus Thermophilus Demonstrate Similarities with Type II Secretion System Pseudopilins
Authors: Karuppiah, V. / Thistlethwaite, A. / Derrick, J.P.
History
DepositionApr 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TYPE-IV LIKE PILIN TTHA1219
B: TYPE-IV LIKE PILIN TTHA1219
C: TYPE-IV LIKE PILIN TTHA1219
D: TYPE-IV LIKE PILIN TTHA1219


Theoretical massNumber of molelcules
Total (without water)100,5074
Polymers100,5074
Non-polymers00
Water10,016556
1
A: TYPE-IV LIKE PILIN TTHA1219
B: TYPE-IV LIKE PILIN TTHA1219


Theoretical massNumber of molelcules
Total (without water)50,2532
Polymers50,2532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-5.8 kcal/mol
Surface area16260 Å2
MethodPISA
2
C: TYPE-IV LIKE PILIN TTHA1219
D: TYPE-IV LIKE PILIN TTHA1219


Theoretical massNumber of molelcules
Total (without water)50,2532
Polymers50,2532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-6.3 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.400, 66.950, 97.470
Angle α, β, γ (deg.)90.00, 99.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A43 - 235
2010B43 - 235
1020A43 - 236
2020C43 - 236
1030A43 - 236
2030D43 - 236
1040B42 - 235
2040C42 - 235
1050B42 - 235
2050D42 - 235
1060C42 - 236
2060D42 - 236

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(0.4911, -0.2417, -0.8369), (-0.3263, -0.9418, 0.0805), (-0.8077, 0.2335, -0.5414)32.815, 26.4601, 49.7223
2given(0.5817, -0.0364, -0.8126), (-0.0837, -0.9964, -0.0153), (-0.8091, 0.0769, -0.5826)28.2388, 57.198, 44.1757
3given(0.9873, 0.1274, 0.0952), (-0.1402, 0.9796, 0.1436), (-0.0749, -0.1551, 0.985)-2.9444, -32.8189, 12.3465

-
Components

#1: Protein
TYPE-IV LIKE PILIN TTHA1219


Mass: 25126.736 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): T7 EXPRESS / References: UniProt: Q5SIZ5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.45 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growDetails: 0.01M ZINC CHLORIDE, 0.1M SODIUM ACETATE PH 5 AND 20% (W/V) PEG 6000

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→35.94 Å / Num. obs: 70620 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
autoSHARPmodel building
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
autoSHARPphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.85→96.23 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.489 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20878 3564 5 %RANDOM
Rwork0.18025 ---
obs0.18173 67037 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.619 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-1.09 Å2
2--0.33 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.85→96.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 0 556 6264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195832
X-RAY DIFFRACTIONr_bond_other_d0.0110.025581
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9867939
X-RAY DIFFRACTIONr_angle_other_deg1.665312823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90523.362232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0211551
X-RAY DIFFRACTIONr_chiral_restr0.1010.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0216699
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6131.9063073
X-RAY DIFFRACTIONr_mcbond_other1.6121.9043072
X-RAY DIFFRACTIONr_mcangle_it2.6582.8423829
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0562.1492759
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A207320.13
12B207320.13
21A211000.11
22C211000.11
31A204800.14
32D204800.14
41B206400.13
42C206400.13
51B206100.13
52D206100.13
61C201880.15
62D201880.15
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 266 -
Rwork0.266 4955 -
obs--99.81 %
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)
11.18320.026-0.32561.10160.21661.7881-0.0690.0161-0.04590.08560.01990.01910.0658-0.07760.04910.04180.0005-0.01450.0043-0.00250.015122.357415.483636.2148
21.3329-0.25370.09621.20940.16460.7855-0.0165-0.02430.07830.0602-0.00120.073-0.0363-0.01350.01770.0171-0.0058-0.00370.00420.00220.01579.59029.904715.324
31.5408-0.0135-0.17991.0119-0.05190.91360.0042-0.05080.07580.05920.02030.0506-0.0328-0.0212-0.02440.0236-0.0028-0.00660.0040.00140.0126.710141.0110.0437
41.03260.09290.18591.23260.22541.3733-0.0141-0.0722-0.04670.0577-0.03680.0509-0.0381-0.07460.05090.06290.0007-0.03250.01320.00040.026516.47846.838332.2492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 236
2X-RAY DIFFRACTION2B42 - 235
3X-RAY DIFFRACTION3C42 - 236
4X-RAY DIFFRACTION4D40 - 236

+
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