[English] 日本語
Yorodumi
- PDB-5xt6: A sulfur-transferring catalytic intermediate of SufS-SufU complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xt6
TitleA sulfur-transferring catalytic intermediate of SufS-SufU complex from Bacillus subtilis
Components
  • (Zinc-dependent sulfurtransferase ...) x 2
  • Cysteine desulfurase SufS
KeywordsBIOSYNTHETIC PROTEIN / Iron-sulfur cluster biosynthesis / SUF machinery / Cysteine desulfurase / Sulfur mobilization / Metalloprotein
Function / homology
Function and homology information


Transferases / cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / iron-sulfur cluster assembly / ferrous iron binding / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / transferase activity / intracellular iron ion homeostasis / cytoplasm
Similarity search - Function
Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / 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 ...Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / 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 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PDA / Zinc-dependent sulfurtransferase SufU / Cysteine desulfurase SufS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsFujishiro, T. / Kunichika, K. / Takahashi, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS15H04472 Japan
JSPS17K14510 Japan
Sumitomo Foundation163037 Japan
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: Zinc-Ligand Swapping Mediated Complex Formation and Sulfur Transfer between SufS and SufU for Iron-Sulfur Cluster Biogenesis in Bacillus subtilis
Authors: Fujishiro, T. / Terahata, T. / Kunichika, K. / Yokoyama, N. / Maruyama, C. / Asai, K. / Takahashi, Y.
History
DepositionJun 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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 / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Zinc-dependent sulfurtransferase SufU
A: Cysteine desulfurase SufS
B: Cysteine desulfurase SufS
C: Zinc-dependent sulfurtransferase SufU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5548
Polymers127,7834
Non-polymers7714
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, homologous to (IscS)2-(IscU)2
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-136 kcal/mol
Surface area37330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.930, 73.930, 367.740
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNGLYGLYDA6 - 1396 - 139
21ASNASNGLYGLYCD6 - 1396 - 139
12METMETTHRTHRAB1 - 4034 - 406
22METMETTHRTHRBC1 - 4034 - 406

NCS ensembles :
ID
1
2

-
Components

-
Zinc-dependent sulfurtransferase ... , 2 types, 2 molecules DC

#1: Protein Zinc-dependent sulfurtransferase SufU / Putative iron-sulfur cluster assembly scaffold protein SufU / Sulfur acceptor protein SufU


Mass: 17256.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sufU, iscU, nifU, yurV, BSU32680 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O32163, Transferases
#3: Protein Zinc-dependent sulfurtransferase SufU / Putative iron-sulfur cluster assembly scaffold protein SufU / Sulfur acceptor protein SufU


Mass: 17288.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sufU, iscU, nifU, yurV, BSU32680 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O32163, Transferases

-
Protein , 1 types, 2 molecules AB

#2: Protein Cysteine desulfurase SufS


Mass: 46618.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sufS, csd, yurW, BSU32690 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: O32164, cysteine desulfurase

-
Non-polymers , 3 types, 7 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PDA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID / PYRIDOXYL-ALANINE-5-PHOSPHATE


Mass: 320.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O7P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Potassium nitrate and 20 % (w/v) PEG3350, 5 mM L-cysteine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1.28229 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 8, 2017 / Details: bending magnet
RadiationMonochromator: fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28229 Å / Relative weight: 1
ReflectionResolution: 3.5→48.29 Å / Num. obs: 27470 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 2.518 % / Biso Wilson estimate: 81.168 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.132 / Rrim(I) all: 0.168 / Χ2: 1.207 / Net I/σ(I): 7.62 / Num. measured all: 69158 / Scaling rejects: 60
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.5-3.62.6020.9841.1521910.4031.23998.2
3.6-3.72.5470.7391.820220.7360.9494.8
3.7-3.82.5920.5972.0617130.7470.75396.7
3.8-3.92.5310.5532.4116020.8060.70193.8
3.9-42.5270.462.813370.8550.58491.5
4-4.12.5130.3133.5413520.8930.39796
4.1-4.22.4260.2653.8911050.9420.33895.8
4.2-4.32.3640.2544.1111140.9180.32496.8
4.3-4.42.2020.1884.8310160.9510.24197.7
4.4-4.52.3410.1615.678710.9710.20398.8
4.5-52.4640.1466.8436050.9770.18498.6
5-62.5310.1267.6239890.9810.15997.9
6-102.6470.0516.643650.9980.06398.8
10-48.292.4480.02234.4111880.9980.02897.3

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J8Q, 2AZH

5j8q

2azh


Resolution: 3.5→48.29 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.919 / SU B: 109.131 / SU ML: 0.703 / SU R Cruickshank DPI: 0.6944 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.741 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 709 5 %RANDOM
Rwork0.2228 ---
obs0.2248 13460 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 353.53 Å2 / Biso mean: 117.295 Å2 / Biso min: 47.01 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å2-1.65 Å20 Å2
2---3.29 Å20 Å2
3---10.68 Å2
Refinement stepCycle: final / Resolution: 3.5→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8396 0 44 3 8443
Biso mean--107.96 66.28 -
Num. residues----1082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198600
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.96111636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90151078
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43625.065383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.579151503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2521538
X-RAY DIFFRACTIONr_chiral_restr0.1050.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216408
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D71100.24
12C71100.24
21A259660.11
22B259660.11
LS refinement shellResolution: 3.5→3.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 50 -
Rwork0.358 956 -
all-1006 -
obs--99.51 %
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)
19.91081.30421.59274.08490.05974.61040.5387-0.1642-0.05820.8251-0.3851-1.50290.5768-0.0069-0.15371.0374-0.0537-0.08530.84940.0010.671322.919-5.5083.611
21.51490.5662-0.79487.62471.27284.5507-0.1823-0.05270.24110.58980.265-0.005-0.09130.2287-0.08270.737-0.0354-0.03640.8881-0.00110.10310.52613.50710.162
33.18260.3915-0.07442.3033-0.09381.6203-0.05330.07510.5114-0.39350.0535-0.2983-0.09130.0279-0.00030.7974-0.11190.04570.81710.04350.14197.88418.603-12.82
412.2834-8.1814-2.631812.309916.217674.8592-0.5804-0.39680.28950.6712-0.1661-0.83061.77891.68090.74650.6457-0.13540.07550.62510.01460.787627.9619.508-2.861
52.77450.68130.37595.0835-0.9323.38820.1350.2428-0.5965-0.05560.0699-0.6040.28890.136-0.20490.9992-0.01230.10480.8262-0.10940.209818.633-8.863-14.985
67.3926-3.05020.24121.88371.03822.0907-0.05380.01280.2223-0.0932-0.15570.0166-0.1542-0.17610.20950.92610.0465-0.03531.09380.00850.14680.94611.73528.684
76.3253-1.152.00116.41474.22456.05380.1871-0.152-0.597-0.2080.2603-0.35290.49880.1192-0.44740.8572-0.18840.07330.81920.09680.11551.186-0.8117.246
81.6371-0.39730.66563.301-0.76062.4034-0.2106-0.23770.46680.12840.10510.6501-0.1053-0.60590.10540.7182-0.1339-0.05361.2683-0.00280.3208-21.35818.9672.023
92.18890.13610.24071.22450.54195.59120.0756-0.2566-0.05190.0360.15730.30770.1667-0.4963-0.23290.8663-0.17450.03590.8890.08180.107-10.7737.3495.726
102.0889-1.3011-0.35321.00860.39450.3248-0.3526-0.54360.37950.24590.12580.0599-0.1879-0.39060.22681.20250.1485-0.15281.7708-0.37560.5263-9.04628.37225.684
119.7321-0.6532.13854.2373-0.37621.2561-0.29780.7690.3162-0.28310.2681-0.0504-0.1226-0.09780.02961.0887-0.06980.07091.0036-0.04930.4288-1.999-21.442-19.366
120.02060.3719-0.512110.7603-14.564719.80390.0821-0.0743-0.00290.1925-0.457-0.1305-0.24890.84840.37491.1192-0.077-0.05521.13630.04930.8606-20.196-22.768-22.897
137.54830.269-2.06475.12332.0293.3-0.57170.7085-0.29520.0090.42360.2868-0.0165-0.42570.14811.1461-0.1004-0.15490.97170.12660.4502-10.153-23.872-13.908
145.27771.0219-6.31220.2289-1.333510.65910.49030.1603-0.49490.1136-0.1127-0.0478-0.1113-0.5273-0.37751.20320.0402-0.09691.0733-0.12250.7779-8.268-30.169-6.815
150.97821.59530.21772.61150.36140.0576-0.26660.2021-0.0237-0.37170.3423-0.0931-0.06340.0199-0.07571.0856-0.08230.02871.09450.05660.5584-5.113-17.51-10.138
16110.3912-50.726455.260829.4284-11.604959.1334-1.2158-1.47892.0854-0.64241.3644-1.6018-4.45720.1503-0.14863.91621.1785-0.48941.8793-0.49930.54189.24138.09530.139
170.44111.0514-0.96612.5865-1.667510.32380.06020.02310.2250.27310.01460.5252-0.7275-0.2895-0.07480.95580.1388-0.18050.965-0.0721.0674-0.48447.28613.817
184.6667-0.5623-1.96175.3228-3.98914.4491-0.56910.56911.49030.22971.20660.4051-0.2615-1.4637-0.63751.6257-0.0852-0.58141.0618-0.15261.56341.72752.6966.98
191.20941.2265-0.73754.20741.98193.00350.6351-0.37980.78210.30870.11320.4836-0.54490.6663-0.74841.4489-0.0106-0.01131.2243-0.17961.3466.12650.01914.45
202.17520.1195-2.65164.6432-2.29354.36350.0936-0.21360.53090.3618-0.1703-1.1301-0.63110.35480.07681.2745-0.0338-0.20071.1096-0.01691.037713.23942.4212.141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 23
2X-RAY DIFFRACTION2A24 - 73
3X-RAY DIFFRACTION3A74 - 291
4X-RAY DIFFRACTION4A292 - 301
5X-RAY DIFFRACTION5A302 - 404
6X-RAY DIFFRACTION6B1 - 25
7X-RAY DIFFRACTION7B26 - 77
8X-RAY DIFFRACTION8B78 - 200
9X-RAY DIFFRACTION9B201 - 315
10X-RAY DIFFRACTION10B316 - 405
11X-RAY DIFFRACTION11C6 - 46
12X-RAY DIFFRACTION12C47 - 55
13X-RAY DIFFRACTION13C56 - 103
14X-RAY DIFFRACTION14C104 - 117
15X-RAY DIFFRACTION15C118 - 140
16X-RAY DIFFRACTION16D6 - 12
17X-RAY DIFFRACTION17D13 - 45
18X-RAY DIFFRACTION18D46 - 67
19X-RAY DIFFRACTION19D68 - 83
20X-RAY DIFFRACTION20D84 - 142

+
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