[English] 日本語
Yorodumi
- PDB-2qar: Structure of the 2TEL crystallization module fused to T4 lysozyme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qar
TitleStructure of the 2TEL crystallization module fused to T4 lysozyme with a helical linker.
Components
  • E80-TELSAM domain
  • Lysozyme
  • TELSAM domain
Keywordshydrolase regulator / polymer / crystallization modules / Sterile Alpha Motif
Function / homology
Function and homology information


Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / viral release from host cell by cytolysis / Signaling by FLT3 fusion proteins / neurogenesis / peptidoglycan catabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific ...Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / hematopoietic stem cell proliferation / viral release from host cell by cytolysis / Signaling by FLT3 fusion proteins / neurogenesis / peptidoglycan catabolic process / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / DNA-binding transcription activator activity, RNA polymerase II-specific / host cell cytoplasm / DNA-binding transcription factor activity, RNA polymerase II-specific / defense response to bacterium / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol
Similarity search - Function
SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. ...SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Sterile alpha motif/pointed domain superfamily / Lysozyme / DNA polymerase; domain 1 / Lysozyme-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AMMONIUM ION / NITRATE ION / Endolysin / Transcription factor ETV6
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNauli, S. / Bowie, J.U.
CitationJournal: Protein Sci. / Year: 2007
Title: Polymer-driven crystallization.
Authors: Nauli, S. / Farr, S. / Lee, Y.J. / Kim, H.Y. / Faham, S. / Bowie, J.U.
History
DepositionJun 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: E80-TELSAM domain
B: TELSAM domain
C: Lysozyme
D: E80-TELSAM domain
E: TELSAM domain
F: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,72316
Polymers78,1916
Non-polymers53210
Water1,38777
1
A: E80-TELSAM domain
B: TELSAM domain
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2386
Polymers39,0953
Non-polymers1423
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: E80-TELSAM domain
E: TELSAM domain
F: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,48610
Polymers39,0953
Non-polymers3907
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.512, 119.512, 58.133
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA19 - 896 - 76
21PROPROLEULEUDD19 - 896 - 76
12SERSERALAALABB15 - 1071 - 93
22SERSERALAALAEE15 - 1071 - 93
13GLYGLYLYSLYSCC1 - 1631 - 163
23GLYGLYLYSLYSFF1 - 1631 - 163

NCS ensembles :
ID
1
2
3

-
Components

-
Protein , 3 types, 6 molecules ADBECF

#1: Protein E80-TELSAM domain


Mass: 9924.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P41212*PLUS
#2: Protein TELSAM domain


Mass: 10694.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P41212*PLUS
#3: Protein Lysozyme / / Lysis protein / Muramidase / Endolysin


Mass: 18477.244 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Production host: Escherichia coli (E. coli) / References: UniProt: P00720*PLUS, lysozyme

-
Non-polymers , 3 types, 87 molecules

#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.06 Å3/Da / Density % sol: 59.86 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→150 Å / Num. obs: 35939 / % possible obs: 99.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.07 / Χ2: 1.09 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.4940.39735671.013198
2.49-2.594.40.35735250.977198.2
2.59-2.74.80.30535891.023198.2
2.7-2.855.30.23935641.037199.1
2.85-3.025.90.18936291.077199.4
3.02-3.266.80.13435921.112199.5
3.26-3.597.30.09336281.153199.9
3.59-4.17.80.06836151.145199.8
4.1-5.1780.05636301.132199.9
5.17-1508.10.04636001.08199.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→103.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 18.777 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.371 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1784 5 %RANDOM
Rwork0.22 ---
obs0.222 35928 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.678 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0.1 Å20 Å2
2---0.19 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→103.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 34 77 5551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0225625
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9587611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7155686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55523.801271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75415975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5171545
X-RAY DIFFRACTIONr_chiral_restr0.0870.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024303
X-RAY DIFFRACTIONr_nbd_refined0.1840.22393
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2126
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.221
X-RAY DIFFRACTIONr_mcbond_it5.35523536
X-RAY DIFFRACTIONr_mcangle_it7.39435460
X-RAY DIFFRACTIONr_scbond_it5.0222408
X-RAY DIFFRACTIONr_scangle_it7.22232150
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A589TIGHT POSITIONAL0.010.05
1A589TIGHT THERMAL0.040.5
2B739TIGHT POSITIONAL0.010.05
2B739TIGHT THERMAL0.040.5
3C1285TIGHT POSITIONAL0.040.05
3C1285TIGHT THERMAL0.020.5
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 135 -
Rwork0.285 2406 -
obs-2541 94.18 %
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)
151.6534-45.213-8.755974.930637.819770.5747-0.00390.5105-2.50322.5757-0.9915-0.8992.2757-2.88710.99540.3015-0.1030.05610.4247-0.17380.392233.2127-31.7222.5723
21.47841.23620.34596.01741.49563.16470.02270.0837-0.10140.0995-0.08230.11030.0373-0.5120.0597-0.1928-0.00450.0548-0.0223-0.0525-0.101540.078-28.132913.9377
37.79342.00030.6754.53650.28472.6695-0.0007-0.03620.21190.0992-0.0453-0.1176-0.4239-0.13850.0459-0.06330.0301-0.0045-0.2536-0.0502-0.178355.56-13.820822.539
48.76517.4999-25.37443.6048-50.562973.45690.19920.48651.4702-0.4851-0.9222-0.9405-1.97392.69520.7230.5545-0.47940.14330.8940.47810.541566.5924-1.28151.1472
56.56250.799-0.10019.425-10.80416.4568-0.96410.6916-0.9138-1.8662-0.0822-1.10512.15520.20161.0463-0.0059-0.09950.34780.05820.0323-0.210792.161814.4415-7.4055
65.94341.6871.1432.04570.29553.137-0.005-0.02570.0648-0.1406-0.05680.155-0.4727-0.25260.0618-0.06910.0922-0.026-0.1621-0.0704-0.0933-4.3558-48.2735-6.4525
77.0217-2.51230.7565.0345-0.34552.57770.15890.17560.0142-0.1851-0.1359-0.4145-0.31270.3795-0.023-0.1845-0.0927-0.0282-0.1283-0.0169-0.127917.5971-55.36490.8681
89.62020.775-9.22386.7597-5.796516.6699-0.78641.9189-1.3535-0.703-0.17760.33411.2449-1.7770.9641-0.05580.07910.20380.088-0.2956-0.229758.6167-72.6387-26.7103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA15 - 182 - 5
2X-RAY DIFFRACTION2AA19 - 916 - 78
3X-RAY DIFFRACTION3BB15 - 941 - 80
4X-RAY DIFFRACTION4BB95 - 10781 - 93
5X-RAY DIFFRACTION5CC1 - 1621 - 162
6X-RAY DIFFRACTION6DD15 - 952 - 82
7X-RAY DIFFRACTION7EE15 - 1071 - 93
8X-RAY DIFFRACTION8FF1 - 1621 - 162

+
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