[English] 日本語
Yorodumi
- PDB-3bzy: Crystal structure of the mutated Y316D EscU C-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bzy
TitleCrystal structure of the mutated Y316D EscU C-terminal domain
Components(EscU) x 2
KeywordsMEMBRANE PROTEIN / PROTEIN TRANSPORT / Auto cleavage protein / flagella / Intein / T3SS / membrane
Function / homology
Function and homology information


dioxygenase activity / protein secretion / isomerase activity / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsZarivach, R. / Deng, W. / Vuckovic, M. / Felise, H.B. / Nguyen, H.V. / Miller, S.I. / Finlay, B.B. / Strynadka, N.C.J.
CitationJournal: Nature / Year: 2008
Title: Structural analysis of the essential self-cleaving type III secretion proteins EscU and SpaS.
Authors: Zarivach, R. / Deng, W. / Vuckovic, M. / Felise, H.B. / Nguyen, H.V. / Miller, S.I. / Finlay, B.B. / Strynadka, N.C.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5203
Polymers15,4242
Non-polymers961
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
MethodPISA
2
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,07912
Polymers61,6958
Non-polymers3844
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area13500 Å2
MethodPISA
3
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0406
Polymers30,8474
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area5530 Å2
MethodPISA
4
A: EscU
B: EscU
hetero molecules

A: EscU
B: EscU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0406
Polymers30,8474
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.882, 58.832, 72.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein EscU


Mass: 5991.751 Da / Num. of mol.: 1 / Fragment: UNP residues 215-262
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EPEC E2348/69 / Gene: escU / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJ26
#2: Protein EscU


Mass: 9431.979 Da / Num. of mol.: 1 / Fragment: UNP residues 263-345 / Mutation: Y316D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: EPEC E2348/69 / Gene: escU / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AJ26
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.92 Å3/Da / Density % sol: 36.05 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: Li2SO4, Bis-Tris, Peg3350, NaCl, pH 5.5, Microbatch, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 37475 / Num. obs: 36351 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.2-1.242.80.3577.7
1.24-1.294.20.30393.9
1.29-1.355.60.25899.5
1.35-1.4270.223100
1.42-1.517.50.15100
1.51-1.637.60.094100
1.63-1.797.70.078100
1.79-2.057.60.065100
2.05-2.597.40.038100
2.59-507.10.02898.2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.2→45.6 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.957 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17801 1824 5 %RANDOM
Rwork0.14226 ---
obs0.14404 34527 96.9 %-
all-37475 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.2→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms897 0 5 115 1017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.022918
X-RAY DIFFRACTIONr_bond_other_d0.0010.02623
X-RAY DIFFRACTIONr_angle_refined_deg3.0322.0251266
X-RAY DIFFRACTIONr_angle_other_deg1.33731566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9145126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.49226.28635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84515184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3152
X-RAY DIFFRACTIONr_chiral_restr0.1670.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021013
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02153
X-RAY DIFFRACTIONr_nbd_refined0.2740.2175
X-RAY DIFFRACTIONr_nbd_other0.1880.2645
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2445
X-RAY DIFFRACTIONr_nbtor_other0.0990.2485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3760.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3780.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4761.5742
X-RAY DIFFRACTIONr_mcbond_other1.5431.5222
X-RAY DIFFRACTIONr_mcangle_it3.942944
X-RAY DIFFRACTIONr_scbond_it6.3423394
X-RAY DIFFRACTIONr_scangle_it7.8574.5313
X-RAY DIFFRACTIONr_rigid_bond_restr3.231824
X-RAY DIFFRACTIONr_sphericity_free17.3843115
X-RAY DIFFRACTIONr_sphericity_bonded7.7931517
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 105 -
Rwork0.244 1924 -
obs--74.46 %

+
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