[English] 日本語
Yorodumi
- PDB-6ckp: Crystal structure of a thioredoxin domain 2 from Brucella meliten... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ckp
TitleCrystal structure of a thioredoxin domain 2 from Brucella melitensis at 1.15 Angstrom resolution
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / SSGCID / Brucella melitensis / Thioredoxin / domain-2 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


protein-disulfide reductase activity / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a thioredoxin domain 2 from Brucella melitensis at 1.15 Angstrom resolution
Authors: Mayclin, S.J. / Dranow, D.M. / Buchko, G.W. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionFeb 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)13,7201
Polymers13,7201
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.240, 40.240, 63.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Thioredoxin


Mass: 13719.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: abortus 2308 / Gene: BK187_10725 / Plasmid: BrabA.00029.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Z1ZP61, UniProt: Q2YQX0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.4 mg/mL BrabA.00029.a.A1.PB00087 with Emerald Biostructures Primary Precipitant #18 (2 M lithium sulfate, 2% PEG400, 100 mM Tris base, pH 8.5), dc, lbx1-3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 8, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 36050 / % possible obs: 100 % / Redundancy: 6.07 % / Biso Wilson estimate: 11.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Χ2: 1.023 / Net I/σ(I): 15.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.15-1.185.9560.5692.7826620.8230.625100
1.18-1.215.9680.4873.3225770.8760.533100
1.21-1.255.9830.4034.0825220.910.442100
1.25-1.296.0070.3394.8424430.9320.371100
1.29-1.336.0390.2785.8723860.9580.304100
1.33-1.376.0850.2287.122830.970.249100
1.37-1.436.1310.1928.4722360.9780.21100
1.43-1.486.1410.14411.121370.9870.158100
1.48-1.556.0790.11613.9320600.9920.12799.9
1.55-1.636.1730.09416.3819280.9940.103100
1.63-1.716.2230.08119.318700.9950.088100
1.71-1.826.1870.06722.8317630.9960.074100
1.82-1.946.1660.05626.4816510.9980.061100
1.94-2.16.0670.0529.9715510.9980.055100
2.1-2.36.0570.04532.2214250.9980.05100
2.3-2.576.0730.04133.5212820.9990.04599.9
2.57-2.976.1180.0435.4411400.9990.04399.9
2.97-3.646.0140.03836.719620.9990.04299.9
3.64-5.146.0150.03537.547530.9980.038100
5.14-40.245.8160.03636.824190.9970.0499.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
Coot3.24model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YJ7

2yj7


Resolution: 1.15→50 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.66
RfactorNum. reflection% reflection
Rfree0.1612 2096 5.81 %
Rwork0.1405 --
obs0.1417 36050 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.84 Å2 / Biso mean: 16.6848 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 0 163 1038
Biso mean---27.98 -
Num. residues----119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.15-1.17680.20261460.18162248
1.1768-1.20620.20231230.16552261
1.2062-1.23880.19261220.15532294
1.2388-1.27530.19371210.14932240
1.2753-1.31640.15971290.14222294
1.3164-1.36350.1721470.13012232
1.3635-1.41810.15561560.12352243
1.4181-1.48260.13381660.11462256
1.4826-1.56080.15881150.1162259
1.5608-1.65860.15851680.11972226
1.6586-1.78670.1521890.12422224
1.7867-1.96640.1491300.12772283
1.9664-2.2510.13491250.12892297
2.251-2.83590.1721370.1582278
2.8359-500.16731220.15052319

+
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