[English] 日本語
Yorodumi
- PDB-5e59: Crystal structure of reduced state of a novel disulfide oxidoredu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5.0E+59
TitleCrystal structure of reduced state of a novel disulfide oxidoreductase from Deinococcus radiodurans
ComponentsFrnE protein
KeywordsOXIDOREDUCTASE / FrnE / Deinococcus / disulfide bond / disulfide isomerase / oxidative stress
Function / homologyDSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / oxidoreductase activity / 3-Layer(aba) Sandwich / Alpha Beta / FrnE protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBihani, S.C. / Panicker, L. / Kumar, V.
CitationJournal: Antioxid. Redox Signal. / Year: 2018
Title: drFrnE Represents a Hitherto Unknown Class of Eubacterial Cytoplasmic Disulfide Oxido-Reductases.
Authors: Bihani, S.C. / Panicker, L. / Rajpurohit, Y.S. / Misra, H.S. / Kumar, V.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FrnE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6783
Polymers28,4941
Non-polymers1842
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint0 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.761, 62.922, 86.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein FrnE protein


Mass: 28493.875 Da / Num. of mol.: 1
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_0659 / Plasmid: pET21b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RWK7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 8000 100mM Sodium Actetate 20% Glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54056 Å
DetectorType: AGILENT TITAN CCD / Detector: CCD / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2→15.76 Å / Num. obs: 18231 / % possible obs: 99.8 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 19.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 9 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 6.1 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata reduction
CrysalisProdata processing
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNW

5cnw


Resolution: 2→15.759 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 915 5.03 %
Rwork0.1572 --
obs0.1596 18200 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→15.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 12 252 2035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071820
X-RAY DIFFRACTIONf_angle_d0.9032466
X-RAY DIFFRACTIONf_dihedral_angle_d14.245661
X-RAY DIFFRACTIONf_chiral_restr0.041262
X-RAY DIFFRACTIONf_plane_restr0.005329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10530.24421430.18242415X-RAY DIFFRACTION100
2.1053-2.23680.21711460.16472402X-RAY DIFFRACTION100
2.2368-2.4090.20681380.17272426X-RAY DIFFRACTION100
2.409-2.65030.2251170.17222459X-RAY DIFFRACTION100
2.6503-3.03150.23951260.16332454X-RAY DIFFRACTION100
3.0315-3.81040.19411200.14242512X-RAY DIFFRACTION100
3.8104-15.75940.17911250.14792617X-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)
11.85040.8250.05322.55970.03381.1209-0.166-0.2148-0.54580.18240.10740.3010.3047-0.1948-0.0110.1955-0.0030.03070.16040.09880.24860.0333143.7646105.0207
24.5656-2.3096-3.07641.18841.59152.3758-0.1402-0.6527-0.38370.13490.14730.17050.23470.0738-0.00680.2112-0.00230.03080.18660.11250.3586-3.7043141.0302112.3656
32.43090.20680.01841.9747-1.56714.4988-0.14660.7817-0.5242-0.48120.0742-0.10430.47940.33120.08830.2729-0.01550.09450.3573-0.0740.250618.1757146.420590.4396
42.3822-0.5569-0.44321.3645-0.60371.88390.04570.75660.027-0.1294-0.01710.068-0.1002-0.1477-0.00760.15450.00310.0130.25520.02490.14258.8095155.201993.0207
51.830.3647-0.47451.4694-0.12272.9795-0.0677-0.5425-0.29810.20390.05380.0403-0.08280.16040.01260.16190.01360.01330.21160.05860.137915.0929149.22109.675
61.636-0.1398-0.43460.1101-0.25591.0346-0.1251-0.6231-0.97330.1163-0.1157-0.14960.52580.5214-0.12120.32790.11320.07330.25620.26030.411317.6258138.4616111.187
70.4885-0.63730.90593.19530.66633.2218-0.05260.1068-0.6451-0.43640.29680.22630.6237-0.3991-0.09680.2817-0.06270.01760.13460.02860.3532-0.7476135.714599.9665
85.86885.9903-5.19838.3566-4.92897.1491-0.18320.3926-0.6595-0.30430.63170.38770.5366-0.6841-0.35930.2519-0.0819-0.03360.23990.09220.3984-12.1414138.4792105.2751
92.224-2.55531.88516.068-1.24231.852-0.0335-0.37260.22770.86630.01450.0753-0.3592-0.0351-0.00420.37110.05750.04860.24640.04030.3946-22.8403119.2822119.874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 109 )
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 185 )
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 207 )
8X-RAY DIFFRACTION8chain 'A' and (resid 208 through 221 )
9X-RAY DIFFRACTION9chain 'A' and (resid 222 through 239 )

+
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