[English] 日本語
Yorodumi
- PDB-7cep: Crystal structure of L-cycloserine-bound form of cysteine desulfu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cep
TitleCrystal structure of L-cycloserine-bound form of cysteine desulfurase SufS from Bacillus subtilis
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / cysteine desulfurase / PLP-dependent enzyme / cysteine metabolism / cycloserine / inhibitor / Fe-S cluster biosynthesis
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-7TS / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsNakamura, R. / Yasuhiro, T. / Fujishiro, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17K14510 Japan
CitationJournal: Febs J. / Year: 2022
Title: Cycloserine enantiomers inhibit PLP-dependent cysteine desulfurase SufS via distinct mechanisms.
Authors: Nakamura, R. / Ogawa, S. / Takahashi, Y. / Fujishiro, T.
History
DepositionJun 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7059
Polymers46,5871
Non-polymers1,1188
Water4,450247
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,40918
Polymers93,1732
Non-polymers2,23616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area10270 Å2
ΔGint2 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.800, 92.800, 128.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Cysteine desulfurase SufS


Mass: 46586.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: O32164, cysteine desulfurase
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-7TS / (5-hydroxy-6-methyl-4-{[(3-oxo-2,3-dihydro-1,2-oxazol-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate


Mass: 331.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Tris-HCl, 50 mM Lithium sulfate, 50%(v/v) PEG200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 25, 2018
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→40.18 Å / Num. obs: 40817 / % possible obs: 100 % / Redundancy: 20.28 % / Biso Wilson estimate: 41.642 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.1 / Χ2: 1.037 / Net I/σ(I): 24.13 / Num. measured all: 827787
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
2.05-2.1521.420.9623.84114963536753670.8910.985100
2.15-2.2521.2630.6795.5594345443744370.950.695100
2.25-2.421.090.4778.06113547538453840.9740.489100
2.4-2.520.8770.35510.6760354289128910.9840.364100
2.5-2.620.6210.26814.0751532249924990.9910.275100
2.6-2.720.2520.22816.0342670210721070.9940.234100
2.7-2.819.8370.19218.5636559184318430.9950.197100
2.8-318.340.14123.5854891299329930.9970.145100
3-3.519.1340.08736.5392209481948190.9990.089100
3.5-419.7180.05753.0353889273427330.9990.059100
4-620.1870.04663.580143397039700.9990.047100
6-1019.3340.03966.72263141361136110.04100
10-40.1815.4260.03367.3963714184130.9990.03498.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZS9

5zs9


Resolution: 2.05→40.18 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 2040 5 %
Rwork0.1656 38771 -
obs0.1667 40811 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.87 Å2 / Biso mean: 44.8675 Å2 / Biso min: 18.05 Å2
Refinement stepCycle: final / Resolution: 2.05→40.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 74 247 3550
Biso mean--60.78 46.8 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.05-2.10.23611350.210225622697
2.1-2.150.22251340.18525482682
2.15-2.210.19221350.180725622697
2.21-2.270.2341330.181125322665
2.27-2.350.23111340.173125422676
2.35-2.430.22121350.17825742709
2.43-2.530.20721350.173825662701
2.53-2.640.22121350.167225692704
2.64-2.780.18541350.172725592694
2.78-2.960.22751350.179625602695
2.96-3.180.22631370.176526002737
3.18-3.50.21541360.171225912727
3.51-4.010.16051370.147526112748
4.01-5.050.13951390.13926352774
5.05-40.180.15491450.171427602905
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)
18.5838-0.0262-0.34162.51310.84360.8836-0.0274-0.22990.47890.19510.04240.4925-0.0077-0.41530.00650.24080.01060.03480.36650.07260.2998-47.211249.142-35.1079
23.4472.4789-1.54846.9068-4.77097.30750.0347-0.3083-0.00430.1434-0.2493-0.3964-0.47520.58040.2380.2274-0.00660.02170.2212-0.06880.1639-21.351654.7243-34.7196
31.97710.26870.12782.7471-0.02151.8063-0.0238-0.4756-0.62670.2186-0.006-0.13970.45830.01290.03210.29890.01040.020.35330.15310.4058-27.586825.7896-27.6497
43.3011-0.878-0.7812.11130.00552.3668-0.0738-0.4694-0.15860.07970.0513-0.35260.09070.38420.00650.1781-0.029-0.02020.28310.03670.2488-16.474541.0559-34.0418
53.06420.4703-0.38463.09420.45681.6039-0.0177-0.0762-0.35290.2163-0.03110.25570.3085-0.47620.05590.2499-0.0580.03260.40270.0940.313-49.885932.0665-32.9165
67.00780.41911.09676.38660.67458.92150.56160.1018-0.6944-0.4076-0.88811.35241.0852-1.58510.41490.3642-0.018-0.04170.7486-0.0070.7814-64.719332.1799-41.3997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 34 )A-1 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 78 )A35 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 224 )A79 - 224
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 295 )A225 - 295
5X-RAY DIFFRACTION5chain 'A' and (resid 296 through 384 )A296 - 384
6X-RAY DIFFRACTION6chain 'A' and (resid 385 through 412 )A385 - 412

+
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