[English] 日本語
Yorodumi
- PDB-5j1m: Crystal structure of Csd1-Csd2 dimer II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j1m
TitleCrystal structure of Csd1-Csd2 dimer II
Components(ToxR-activated gene (TagE)) x 2
KeywordsHYDROLASE / M23B family metallopeptidase / Heterodimer
Function / homology: / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / metalloendopeptidase activity / membrane / metal ion binding / ToxR-activated gene (TagE) / ToxR-activated gene (TagE)
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsAn, D.R. / Suh, S.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation2013R1A2A1A05067303 Korea, Republic Of
CitationJournal: Plos One / Year: 2016
Title: Structural Basis of the Heterodimer Formation between Cell Shape-Determining Proteins Csd1 and Csd2 from Helicobacter pylori
Authors: An, D.R. / Im, H.N. / Jang, J.Y. / Kim, H.S. / Kim, J. / Yoon, H.J. / Hesek, D. / Lee, M. / Mobashery, S. / Kim, S.J. / Suh, S.W.
History
DepositionMar 29, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
A: ToxR-activated gene (TagE)
B: ToxR-activated gene (TagE)
C: ToxR-activated gene (TagE)
D: ToxR-activated gene (TagE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0506
Polymers91,9194
Non-polymers1312
Water2,522140
1
A: ToxR-activated gene (TagE)
B: ToxR-activated gene (TagE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0253
Polymers45,9602
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-24 kcal/mol
Surface area14680 Å2
MethodPISA
2
C: ToxR-activated gene (TagE)
D: ToxR-activated gene (TagE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0253
Polymers45,9602
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-64 kcal/mol
Surface area14340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.149, 80.013, 74.594
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ToxR-activated gene (TagE)


Mass: 24612.207 Da / Num. of mol.: 2 / Fragment: UNP residues 125-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_1543 / Production host: Escherichia coli (E. coli) / References: UniProt: O26068
#2: Protein ToxR-activated gene (TagE)


Mass: 21347.436 Da / Num. of mol.: 2 / Fragment: UNP residues 121-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_1544 / Production host: Escherichia coli (E. coli) / References: UniProt: O26069
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 1.67 Å3/Da / Density % sol: 26.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: HEPES, Jeffamine ED-2001

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→50.01 Å / Num. obs: 25521 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 26.6
Reflection shellResolution: 2.35→2.39 Å / Mean I/σ(I) obs: 3.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.926 / SU B: 7.262 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.709 / ESU R Free: 0.268 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23281 1246 4.9 %RANDOM
Rwork0.16771 ---
obs0.17103 24021 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.958 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20.34 Å2
2---0.17 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.35→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 2 140 5560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195557
X-RAY DIFFRACTIONr_bond_other_d0.0020.025356
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9427510
X-RAY DIFFRACTIONr_angle_other_deg0.926312315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79224.286252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54815964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3131520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216252
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021344
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_it2.6324.2192706
X-RAY DIFFRACTIONr_mcbond_other2.6314.2172705
X-RAY DIFFRACTIONr_mcangle_it4.1036.3043372
X-RAY DIFFRACTIONr_mcangle_other4.1036.3063373
X-RAY DIFFRACTIONr_scbond_it3.0714.662851
X-RAY DIFFRACTIONr_scbond_other3.0724.6562849
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9636.8014138
X-RAY DIFFRACTIONr_long_range_B_refined7.38833.6196212
X-RAY DIFFRACTIONr_long_range_B_other7.38633.6066189
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 78 -
Rwork0.216 1755 -
obs--97.71 %

+
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