[English] 日本語
Yorodumi
- PDB-3t7y: Structure of an autocleavage-inactive mutant of the cytoplasmic d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t7y
TitleStructure of an autocleavage-inactive mutant of the cytoplasmic domain of CT091, the YscU homologue of Chlamydia trachomatis
ComponentsYop proteins translocation protein U
KeywordsPROTEIN TRANSPORT / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta / self-cleaving / type III secretion system / transmembrane / inner membrane / cytoplasmic domain
Function / homology
Function and homology information


protein secretion / membrane => GO:0016020 / plasma membrane
Similarity search - Function
secretion proteins EscU / name from scop / Type III exporter system, secretion apparatus protein BsaZ / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / SUCCINIC ACID / Yop proteins translocation protein U
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSinger, A.U. / Wawrzak, Z. / Skarina, T. / Saikali, P. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Structure of an autocleavage-inactive mutant of the cytoplasmic domain of CT091, the YscU homologue of Chlamydia trachomatis
Authors: Singer, A.U. / Wawrzak, Z. / Skarina, T. / Saikali, P. / Anderson, W.F. / Savchenko, A.
History
DepositionJul 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Yop proteins translocation protein U
B: Yop proteins translocation protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,15518
Polymers21,4472
Non-polymers70816
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-49 kcal/mol
Surface area10470 Å2
MethodPISA
2
A: Yop proteins translocation protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1209
Polymers10,7241
Non-polymers3968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Yop proteins translocation protein U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0359
Polymers10,7241
Non-polymers3128
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.365, 68.365, 37.335
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 249:342 )
211chain B and (resseq 249:342 )
DetailsThe dimeric structure is dependent in this crystal form on the ions and therefore it could also be monomeric.

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Yop proteins translocation protein U


Mass: 10723.506 Da / Num. of mol.: 2 / Fragment: sequence database residues 249-345 / Mutation: N263A
Source method: isolated from a genetically manipulated source
Details: Cut with TEV during purification, but then papain added to crystallization setup
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: D/UW-3/CX / Gene: CT_091, yscU / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold magic / References: UniProt: O84093

-
Non-polymers , 5 types, 95 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% Tacsimate,1% DMSO 0.1 M Hepes pH 7.5 plus 0.1 mg/ml papain. Cryoprotected with 40% tacsimate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2010 / Details: Mirrors
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 13224 / Num. obs: 12628 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 27.875
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.213 / % possible all: 63.9

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swiss-prot model from PDB 3BZP

3bzp


Resolution: 2.1→31.58 Å / SU ML: 0.54 / σ(F): 2.01 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 547 4.85 %
Rwork0.1881 --
obs0.1897 11286 99.01 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.01 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1097 Å20 Å20 Å2
2---0.1097 Å20 Å2
3---0.2194 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 41 79 1564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081594
X-RAY DIFFRACTIONf_angle_d1.2682163
X-RAY DIFFRACTIONf_dihedral_angle_d16.794597
X-RAY DIFFRACTIONf_chiral_restr0.072249
X-RAY DIFFRACTIONf_plane_restr0.004276
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A739X-RAY DIFFRACTIONPOSITIONAL
12B739X-RAY DIFFRACTIONPOSITIONAL0.081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.31130.22731340.19692605X-RAY DIFFRACTION96
2.3113-2.64560.22591480.20222715X-RAY DIFFRACTION100
2.6456-3.33260.24661200.19682712X-RAY DIFFRACTION100
3.3326-31.58390.21241450.17642707X-RAY DIFFRACTION100
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)
12.9008-1.2670.07356.00530.10634.01770.00090.13780.3898-0.1821-0.0507-0.0503-0.2848-0.05290.04230.1305-0.02740.02110.1677-0.00070.1268-2.141812.999-1.4948
26.87111.06940.1993.21810.38564.87640.0055-0.23940.1980.1045-0.0221-0.3379-0.07040.31580.01180.15890.00890.01270.1171-0.01040.1283-21.705924.23292.2282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 230:360)
2X-RAY DIFFRACTION2(chain B and resid 230:360)

+
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