[English] 日本語
Yorodumi
- PDB-6uy5: E. coli cysteine desulfurase SufS with a spontaneously rotated be... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uy5
TitleE. coli cysteine desulfurase SufS with a spontaneously rotated beta-hairpin
ComponentsCysteine desulfurase
KeywordsLyase / Transferase / cysteine desulfurase / SufS / persulfide / PLP
Function / homology
Function and homology information


selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / sulfur compound metabolic process / iron-sulfur cluster assembly ...selenium compound metabolic process / Hydrolases; Acting on carbon-sulfur bonds; Acting on carbon-sulfur bonds / cysteine sulfinate desulfinase activity / selenocysteine lyase / selenocysteine lyase activity / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / sulfur compound metabolic process / iron-sulfur cluster assembly / pyridoxal phosphate binding / hydrolase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Cysteine desulfurase, SufS / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Cysteine desulfurase, SufS / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsDunkle, J.A. / Frantom, P.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM112919 United States
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2020
Title: Structural evidence for a latch mechanism regulating access to the active site of SufS-family cysteine desulfurases
Authors: Dunkle, J.A. / Bruno, M.R. / Frantom, P.A.
History
DepositionNov 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5204
Polymers89,0252
Non-polymers4942
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-31 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.540, 115.740, 63.660
Angle α, β, γ (deg.)90.000, 114.470, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cysteine desulfurase / Selenocysteine beta-lyase / SCL / Selenocysteine lyase / Selenocysteine reductase


Mass: 44512.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: sufS, csdB, ynhB, b1680, JW1670 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P77444, cysteine desulfurase, selenocysteine lyase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M MgCl2, 0.1M Bis-Tris HCl pH 5.5, 23.3% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→32.253 Å / Num. obs: 125851 / % possible obs: 99 % / Redundancy: 3.298 % / Biso Wilson estimate: 30.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.077 / Χ2: 1.074 / Net I/σ(I): 10.92 / Num. measured all: 415026 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.3471.2730.931048935392750.3031.51999.2
1.54-1.583.4041.0541.1930996914891050.4271.25399.5
1.58-1.633.3740.871.5229823890488400.5531.03699.3
1.63-1.683.310.6991.9228373866785730.6570.83698.9
1.68-1.733.2410.5542.4726754835482540.7820.66698.8
1.73-1.793.1020.4263.1624520804279050.8620.51598.3
1.79-1.862.9710.3264.1522964788277290.9020.39698.1
1.86-1.943.4250.2846.4125537749674550.9130.3499.5
1.94-2.023.4920.228.6625154724372040.9340.26299.5
2.02-2.123.4650.1611.2523769688268590.9630.19199.7
2.12-2.243.4030.12313.5122307658965560.9750.14799.5
2.24-2.373.3160.09116.0520481621361760.9850.1199.4
2.37-2.543.0890.07317.7817839585057750.990.08898.7
2.54-2.743.2230.05721.4717290543153640.9940.06998.8
2.74-33.4270.04625.4717075501549820.9960.05599.3
3-3.363.3440.03729.1415088457045120.9970.04498.7
3.36-3.883.260.03133.3412771398839170.9980.03898.2
3.88-4.753.0190.02735.0710040340033260.9980.03297.8
4.75-6.713.2220.02535.988371265025980.9980.0398
6.71-32.2533.3370.02338.854826147514460.9990.02798

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1jf9

1jf9


Resolution: 1.501→32.253 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.29
RfactorNum. reflection% reflection
Rfree0.2206 2008 1.6 %
Rwork0.1968 --
obs0.1972 125794 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.55 Å2 / Biso mean: 27.8656 Å2 / Biso min: 14.91 Å2
Refinement stepCycle: final / Resolution: 1.501→32.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6190 0 30 311 6531
Biso mean--25.28 30.57 -
Num. residues----804
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.501-1.53850.33521360.3178878199
1.5385-1.58010.34091530.3048819100
1.5801-1.62660.32431360.3005887099
1.6266-1.67910.29471490.3027884699
1.6791-1.73910.30991320.3053878699
1.7391-1.80870.31651540.303875798
1.8087-1.8910.3111410.2813880199
1.891-1.99070.25881490.21398838100
1.9907-2.11540.24671420.19788898100
2.1154-2.27870.20881420.19128913100
2.2787-2.5080.19761390.1918886699
2.508-2.87070.22711420.1968885399
2.8707-3.6160.21521440.1843886899
3.616-32.250.15721490.1413889098
Refinement TLS params.Method: refined / Origin x: 5.8363 Å / Origin y: 2.0955 Å / Origin z: 15.8228 Å
111213212223313233
T0.1688 Å2-0.0104 Å2-0.0048 Å2-0.202 Å2-0.0021 Å2--0.1734 Å2
L0.2085 °2-0.1165 °2-0.0166 °2-0.6871 °2-0.1531 °2--0.2569 °2
S0.0249 Å °0.0203 Å °0.0017 Å °-0.0292 Å °-0.0664 Å °-0.0356 Å °0.0035 Å °0.0464 Å °0.043 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 406
2X-RAY DIFFRACTION1allA407 - 1099
3X-RAY DIFFRACTION1allB2 - 406
4X-RAY DIFFRACTION1allB407 - 1097

+
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