[English] 日本語
Yorodumi
- PDB-7dka: Crystal structure of DsbA-like protein DR2335 from Deinococcus ra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dka
TitleCrystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, C24S mutant protein
ComponentsDSBA domain-containing protein
KeywordsOXIDOREDUCTASE / DsbA / thioredoxin fold / Thiol:disulfide interchange protein
Function / homologyDSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin-like superfamily / oxidoreductase activity / ACETATE ION / DI(HYDROXYETHYL)ETHER / DSBA domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKim, M.-K. / Zhang, J. / Zhao, L.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1F1A1057780 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native protein
Authors: Kim, M.-K. / Zhang, J. / Zhao, L.
History
DepositionNov 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DSBA domain-containing protein
B: DSBA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,74719
Polymers52,4762
Non-polymers1,27117
Water9,476526
1
A: DSBA domain-containing protein
hetero molecules

B: DSBA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,74719
Polymers52,4762
Non-polymers1,27117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
Buried area6780 Å2
ΔGint-6 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.084, 84.177, 63.898
Angle α, β, γ (deg.)90.000, 91.540, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DSBA domain-containing protein


Mass: 26238.105 Da / Num. of mol.: 2 / Mutation: C24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_2335 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RRZ4
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 295 K / Method: microbatch
Details: Ammonium acetate, Sodium acetate trihydrate pH 4.6, 30% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 67292 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.055 / Rrim(I) all: 0.15 / Rsym value: 0.139 / Net I/σ(I): 37.635
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 4.845 / Num. unique obs: 3334 / CC1/2: 0.839 / Rpim(I) all: 0.31 / Rrim(I) all: 0.842 / Rsym value: 0.782

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DK9

7dk9


Resolution: 1.56→29.86 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 1998 2.97 %
Rwork0.1554 65258 -
obs0.1562 67256 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.4 Å2 / Biso mean: 19.9027 Å2 / Biso min: 6.16 Å2
Refinement stepCycle: final / Resolution: 1.56→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 85 526 3973
Biso mean--38.66 32.64 -
Num. residues----421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.60.2231390.20324567470698
1.6-1.650.20841500.189846634813100
1.65-1.690.22741330.188746034736100
1.69-1.750.2061470.184246634810100
1.75-1.810.23531430.176346534796100
1.81-1.880.24521410.171546684809100
1.88-1.970.18941430.161246484791100
1.97-2.070.20571410.160346734814100
2.07-2.20.1841420.150746774819100
2.2-2.370.19031480.151746644812100
2.37-2.610.13871440.150246474791100
2.61-2.990.18361390.151947074846100
2.99-3.760.14661470.139946964843100
3.77-29.860.17081410.14644729487099

+
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