[English] 日本語
Yorodumi
- PDB-2iy2: Crystal structure of the N-terminal dimer domain of E.coli DsbG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iy2
TitleCrystal structure of the N-terminal dimer domain of E.coli DsbG
ComponentsTHIOL DISULFIDE INTERCHANGE PROTEIN DSBG
KeywordsCHAPERONE / DSBC / DSBG / PERIPLASMIC / REDOX-ACTIVE CENTER / DISULFIDE BOND ISOMERASE
Function / homology
Function and homology information


protein disulfide isomerase activity / : / outer membrane-bounded periplasmic space / protein homodimerization activity
Similarity search - Function
Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Nuclear Transport Factor 2; Chain: A, / Thioredoxin-like superfamily ...Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase, DsbC/G / Disulfide bond isomerase protein N-terminal domain / : / Thioredoxin-like domain / Thioredoxin-like fold / Nuclear Transport Factor 2; Chain: A, / Thioredoxin-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Thiol:disulfide interchange protein DsbG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYeh, S.-M. / Metcalf, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Structures of the Dimerization Domains of the Escherichia Coli Disulfide-Bond Isomerase Enzymes Dsbc and Dsbg
Authors: Yeh, S.-M. / Koon, N. / Squire, C. / Metcalf, P.
History
DepositionJul 12, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOL DISULFIDE INTERCHANGE PROTEIN DSBG
B: THIOL DISULFIDE INTERCHANGE PROTEIN DSBG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3126
Polymers15,8622
Non-polymers4504
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.842, 56.842, 42.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein THIOL DISULFIDE INTERCHANGE PROTEIN DSBG / DSBG


Mass: 7931.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: FOUR CADMIUM INOS COORDINATE WITH WATER MOLECULES AND SIDE CHAINS OF ASP46 OR HIS49 ON BOTH CHAINS
Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P77202
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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 Å3/Da / Density % sol: 39.4 %
Description: DIFFRACTION QUALITY WAS IMPROVED USING THE FLASH- ANNEALING METHOD.
Crystal growpH: 7.5 / Details: 0.2M CADMIUM CHLORIDE, 33% MPD, pH 7.50

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→34 Å / Num. obs: 10806 / % possible obs: 99.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.3 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V58

1v58


Resolution: 1.9→56.79 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.404 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 512 4.8 %RANDOM
Rwork0.196 ---
obs0.198 10136 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→56.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 4 58 1071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221028
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9951387
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.125133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.13825.75833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15315177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02746
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2410
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2716
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.215
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8381.5686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24321065
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2283395
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1044.5322
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
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 40
Rwork0.187 736
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)
12.76530.403-0.9754.0484-0.8134.70770.026-0.1812-0.1860.3782-0.0325-0.2530.02350.31490.00650.02280.0162-0.05780.0049-0.03230.0153-13.68813.4914.011
23.87980.0617-0.55244.35690.47866.1189-0.00590.3385-0.3197-0.35390.1149-0.21670.19980.2832-0.109-0.02120.0061-0.01170.0012-0.0714-0.0215-17.8989.955-10.711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 71
2X-RAY DIFFRACTION2B3 - 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