[English] 日本語
Yorodumi
- PDB-9jxt: An aldehyde-containing intermediate of SufS in complex with (2R,3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jxt
TitleAn aldehyde-containing intermediate of SufS in complex with (2R,3R)-3-ethoxycarbonylaziridine-2-carboxylic acid
ComponentsCysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / Cysteine desulfurase
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
: / DI(HYDROXYETHYL)ETHER / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNakamura, R. / Fujishiro, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04542 Japan
New Energy and Industrial Technology Development Organization (NEDO)22100875-0 Japan
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Discovery of an Aziridine-Based Inhibitor That Targets Cysteine Desulfurase Type II SufS via High-Throughput X-ray Crystallography
Authors: Fujishiro, T. / Otsuka, H. / Nakamura, R. / Fujihara, T.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0253
Polymers46,5871
Non-polymers4382
Water2,954164
1
A: Cysteine desulfurase SufS
hetero molecules

A: Cysteine desulfurase SufS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0506
Polymers93,1732
Non-polymers8774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area7480 Å2
ΔGint-21 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.700, 92.700, 128.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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)
Gene: sufS, csd, yurW, BSU32690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O32164, cysteine desulfurase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-A1L40 / (2~{S})-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-oxidanylidene-propanoic acid


Mass: 332.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N2O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64 %
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: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 32955 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Net I/σ(I): 23.67
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.30.83240370.8280.8771
2.3-2.40.61734130.880.6511
2.4-2.50.47928840.9320.5051
2.5-2.60.32824650.9720.3461
2.6-2.70.27321130.9820.2871
2.7-2.80.21818450.9870.231
2.8-2.90.17615700.9910.1851
2.9-30.13114000.9950.1381
3-3.10.10712140.9960.1141
3.1-3.30.08120140.9980.0861
3.3-3.50.06115780.9990.0641
3.5-40.04427220.9990.0461
4-4.50.03416480.9990.0361
4.5-50.0310650.9990.0311
5-60.029122210.0311
6-100.023135710.0241
10-500.01740810.0181

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KFY

6kfy


Resolution: 2.2→46.35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.028 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21223 1648 5 %RANDOM
Rwork0.1741 ---
obs0.17602 31304 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.817 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å2-0 Å2
2---0.09 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.2→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 29 164 3366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123288
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.834468
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.636514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0610548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.120.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022500
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.353.5961636
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3126.4342043
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1733.9421652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.67545.4114342
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 120 -
Rwork0.242 2286 -
obs--100 %
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)
10.0320.1163-0.02841.01710.25720.70720.0616-0.026-0.0090.0958-0.0907-0.0285-0.02180.14540.0290.1579-0.0451-0.00390.1208-0.01110.0469-28.46566.629-15.2125
20.1652-0.01040.04610.61540.06450.35970.1461-0.02760.00780.1925-0.1930.23610.02450.02580.04680.2004-0.09850.08910.0801-0.08080.1039-52.22824.1629-8.105
30.2105-0.0159-0.12840.94030.59550.47790.1068-0.09190.0802-0.0384-0.12030.1213-0.16580.01190.01350.2523-0.12010.07030.0895-0.06560.0536-38.337930.0058-13.2396
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 56
2X-RAY DIFFRACTION2A57 - 300
3X-RAY DIFFRACTION3A301 - 406

+
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