[English] 日本語
Yorodumi
- PDB-4pdx: Crystal structure of Escherchia coli uncharacterized protein YjcS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pdx
TitleCrystal structure of Escherchia coli uncharacterized protein YjcS
ComponentsPutative alkyl/aryl-sulfatase YjcS
KeywordsHYDROLASE / alkylsulfatase
Function / homology
Function and homology information


linear primary-alkylsulfatase activity / dodecyl sulfate metabolic process / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / outer membrane-bounded periplasmic space / protein dimerization activity
Similarity search - Function
Alkyl sulfatase, dimerisation domain / Metallo-beta-lactamase domain / Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl sulfatase dimerisation / Alkyl sulfatase C-terminal / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily ...Alkyl sulfatase, dimerisation domain / Metallo-beta-lactamase domain / Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl sulfatase dimerisation / Alkyl sulfatase C-terminal / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative alkyl/aryl-sulfatase YjcS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsLiang, Y.J. / Gao, Z.Q. / Liu, Q.S. / Dong, Y.H.
CitationJournal: To Be Published
Title: Crystal structure of Escherchia coli uncharacterized protein YjcS
Authors: Liang, Y.J. / Gao, Z.Q. / Dong, Y.H. / Liu, Q.S.
History
DepositionApr 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative alkyl/aryl-sulfatase YjcS
B: Putative alkyl/aryl-sulfatase YjcS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3617
Polymers143,8892
Non-polymers4725
Water19,4741081
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11320 Å2
ΔGint-93 kcal/mol
Surface area44520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.550, 76.182, 103.681
Angle α, β, γ (deg.)90.00, 115.26, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Putative alkyl/aryl-sulfatase YjcS


Mass: 71944.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yjcS, b4083, JW5721 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P32717, Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1081 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.8M (NH4)2SO4, 2% PEG 400, 0.1M HEPES (pH 7.5)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 131954 / Num. obs: 131954 / % possible obs: 98.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.151 / Net I/σ(I): 36.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 5.2 / % possible all: 97.4

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.75→45.118 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 6591 5.05 %Random selection
Rwork0.1829 ---
obs0.1846 130555 92.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→45.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9751 0 27 1081 10859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079968
X-RAY DIFFRACTIONf_angle_d1.07613514
X-RAY DIFFRACTIONf_dihedral_angle_d13.7873612
X-RAY DIFFRACTIONf_chiral_restr0.0751465
X-RAY DIFFRACTIONf_plane_restr0.0051760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.30552220.26064048X-RAY DIFFRACTION91
1.7699-1.79070.25642240.2424134X-RAY DIFFRACTION93
1.7907-1.81260.27762060.23714183X-RAY DIFFRACTION93
1.8126-1.83550.26572100.21884154X-RAY DIFFRACTION93
1.8355-1.85960.27722080.21014177X-RAY DIFFRACTION93
1.8596-1.88510.26372100.20284113X-RAY DIFFRACTION93
1.8851-1.91210.22652110.1914150X-RAY DIFFRACTION93
1.9121-1.94060.22312140.18794130X-RAY DIFFRACTION92
1.9406-1.97090.24131990.18724140X-RAY DIFFRACTION92
1.9709-2.00320.21862230.18384123X-RAY DIFFRACTION92
2.0032-2.03780.21472240.17834096X-RAY DIFFRACTION92
2.0378-2.07480.22072220.18014105X-RAY DIFFRACTION92
2.0748-2.11470.22682220.18264137X-RAY DIFFRACTION92
2.1147-2.15790.22392290.17764099X-RAY DIFFRACTION92
2.1579-2.20480.22782210.17044056X-RAY DIFFRACTION91
2.2048-2.25610.20212300.17744152X-RAY DIFFRACTION92
2.2561-2.31250.23522130.17534110X-RAY DIFFRACTION92
2.3125-2.3750.20252390.17614175X-RAY DIFFRACTION93
2.375-2.44490.22692350.17724141X-RAY DIFFRACTION93
2.4449-2.52380.20622250.18094190X-RAY DIFFRACTION93
2.5238-2.6140.2352110.18334219X-RAY DIFFRACTION94
2.614-2.71870.21442340.18094183X-RAY DIFFRACTION94
2.7187-2.84240.22032270.19254179X-RAY DIFFRACTION94
2.8424-2.99220.22042080.1854202X-RAY DIFFRACTION93
2.9922-3.17970.22672130.18844162X-RAY DIFFRACTION92
3.1797-3.42510.20062380.18114086X-RAY DIFFRACTION91
3.4251-3.76960.21472090.16694070X-RAY DIFFRACTION90
3.7696-4.31470.17842080.16174123X-RAY DIFFRACTION91
4.3147-5.43460.17412240.16184092X-RAY DIFFRACTION90
5.4346-45.1330.21152320.19924035X-RAY DIFFRACTION87

+
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://pdbjlvh1.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