[English] 日本語
Yorodumi
- PDB-6uxt: Crystal structure of unknown function protein yfdX from Shigella ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uxt
TitleCrystal structure of unknown function protein yfdX from Shigella flexneri
ComponentsYfdX protein
KeywordsSTRUCTURAL GENOMICS / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


YfdX protein domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2140 / Uncharacterised protein family YfdX / YfdX protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / YfdX family protein
Similarity search - Component
Biological speciesShigella flexneri 2a str. 2457T (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.797 Å
AuthorsChang, C. / Skarina, T. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of unknown function protein yfdX from Shigella flexneri
Authors: Chang, C. / Skarina, T. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: YfdX protein
B: YfdX protein
C: YfdX protein
D: YfdX protein
E: YfdX protein
F: YfdX protein
G: YfdX protein
H: YfdX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,02812
Polymers162,3838
Non-polymers6454
Water13,565753
1
A: YfdX protein
B: YfdX protein
C: YfdX protein
D: YfdX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4486
Polymers81,1914
Non-polymers2562
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11570 Å2
ΔGint-57 kcal/mol
Surface area27670 Å2
MethodPISA
2
E: YfdX protein
F: YfdX protein
G: YfdX protein
H: YfdX protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5806
Polymers81,1914
Non-polymers3882
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-49 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.579, 92.920, 93.469
Angle α, β, γ (deg.)97.350, 98.440, 95.460
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
YfdX protein


Mass: 20297.846 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri 2a str. 2457T (bacteria)
Gene: yfdX, / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Y2P124
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG3350, 0.2M ammonium citrate, 50mM MES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.797→50 Å / Num. obs: 143645 / % possible obs: 91.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.037 / Rrim(I) all: 0.073 / Χ2: 0.861 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.50.47771830.8230.2960.5620.44691.4
1.83-1.863.60.40672150.8830.2480.4770.47191.6
1.86-1.93.60.3471560.9080.2060.3980.49891.1
1.9-1.943.70.27772000.9420.1670.3240.5291.6
1.94-1.983.70.24370290.9520.1460.2840.55389.4
1.98-2.033.70.269470.9670.120.2340.57589.2
2.03-2.083.60.16666690.9730.10.1950.65583.8
2.08-2.133.70.1572640.9780.090.1750.65793.1
2.13-2.23.70.12873250.9840.0770.1490.72894
2.2-2.273.70.11373320.9850.0680.1320.81492.3
2.27-2.353.80.171510.9860.060.1170.79991
2.35-2.443.70.08971150.9890.0530.1040.84790.7
2.44-2.553.70.08168470.9910.0480.0940.89787.4
2.55-2.693.80.07474630.9910.0440.0860.91594.7
2.69-2.863.80.06773840.9930.040.0780.96493.7
2.86-3.083.80.06272420.9940.0360.0721.11892.5
3.08-3.393.80.05570370.9940.0330.0641.389.7
3.39-3.883.80.04975060.9960.0290.0571.39195.4
3.88-4.883.80.04670940.9960.0270.0531.44290.3
4.88-503.80.04574860.9970.0270.0531.39895.3

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A02

6a02


Resolution: 1.797→43.517 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.91
RfactorNum. reflection% reflection
Rfree0.2003 7201 5.01 %
Rwork0.1701 --
obs0.1716 143610 91.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.5 Å2 / Biso mean: 32.3239 Å2 / Biso min: 15.35 Å2
Refinement stepCycle: final / Resolution: 1.797→43.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10010 0 42 753 10805
Biso mean--56.44 36.25 -
Num. residues----1306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.797-1.81690.36592320.2962414083
1.8169-1.83830.32112550.2729455191
1.8383-1.86070.26892400.2398455492
1.8607-1.88430.24452440.2235457092
1.8843-1.90910.25692620.2074447390
1.9091-1.93520.22612250.1911460892
1.9352-1.96290.22522100.1838451290
1.9629-1.99220.24882210.1808449089
1.9922-2.02330.22692060.178442389
2.0233-2.05650.21772060.174411181
2.0565-2.09190.22392560.175450092
2.0919-2.130.21562430.179464293
2.13-2.1710.23092400.1799469894
2.171-2.21530.2252660.1784460992
2.2153-2.26340.20332780.1723459393
2.2634-2.31610.20552430.1665454492
2.3161-2.3740.21022250.17461192
2.374-2.43820.21372670.1766444689
2.4382-2.50990.21542470.1807415784
2.5099-2.59090.20092410.1748470794
2.5909-2.68350.20362790.1703472195
2.6835-2.79090.18482200.1713469994
2.7909-2.91790.21462550.1781465193
2.9179-3.07170.21772510.1872458092
3.0717-3.26410.20132320.1734427486
3.2641-3.5160.19762280.1731481296
3.516-3.86970.17192430.1582479196
3.8697-4.42920.15912190.1387467493
4.4292-5.57840.17772120.1499459092
5.5784-43.5170.17372550.1549467894

+
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