[English] 日本語
Yorodumi
- PDB-5coj: Structure of Hydroxyethylthiazole kinase ThiM from Staphylococcus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5coj
TitleStructure of Hydroxyethylthiazole kinase ThiM from Staphylococcus aureus in complex with native substrate 2-(4-methyl-1,3-thiazol-5-yl)ethanol.
ComponentsHydroxyethylthiazole kinase
KeywordsTRANSFERASE / Bacterial Thiamine Biosynthesis / Hydroxyethylthiazole kinase / 2-(4-methyl-1 / 3-thiazol-5-yl)ethanol
Function / homology
Function and homology information


hydroxyethylthiazole kinase / hydroxyethylthiazole kinase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / phosphorylation / magnesium ion binding / ATP binding
Similarity search - Function
Hydroxyethylthiazole kinase / Hydroxyethylthiazole kinase family / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-(4-METHYL-THIAZOL-5-YL)-ETHANOL / Hydroxyethylthiazole kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsDrebes, J. / Kuenz, M. / Eberle, R.J. / Oberthuer, D. / Cang, H. / Wrenger, C. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
LEXI-SDI Germany
CitationJournal: Sci Rep / Year: 2016
Title: Structure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.
Authors: Julia Drebes / Madeleine Künz / Björn Windshügel / Alexey G Kikhney / Ingrid B Müller / Raphael J Eberle / Dominik Oberthür / Huaixing Cang / Dmitri I Svergun / Markus Perbandt / ...Authors: Julia Drebes / Madeleine Künz / Björn Windshügel / Alexey G Kikhney / Ingrid B Müller / Raphael J Eberle / Dominik Oberthür / Huaixing Cang / Dmitri I Svergun / Markus Perbandt / Christian Betzel / Carsten Wrenger /
Abstract: Infections caused by the methicillin-resistant Staphylococcus aureus (MRSA) are today known to be a substantial threat for global health. Emerging multi-drug resistant bacteria have created a ...Infections caused by the methicillin-resistant Staphylococcus aureus (MRSA) are today known to be a substantial threat for global health. Emerging multi-drug resistant bacteria have created a substantial need to identify and discover new drug targets and to develop novel strategies to treat bacterial infections. A promising and so far untapped antibiotic target is the biosynthesis of vitamin B1 (thiamin). Thiamin in its activated form, thiamin pyrophosphate, is an essential co-factor for all organisms. Therefore, thiamin analogous compounds, when introduced into the vitamin B1 biosynthetic pathway and further converted into non-functional co-factors by the bacterium can function as pro-drugs which thus block various co-factor dependent pathways. We characterized one of the key enzymes within the S. aureus vitamin B1 biosynthetic pathway, 5-(hydroxyethyl)-4-methylthiazole kinase (SaThiM; EC 2.7.1.50), a potential target for pro-drug compounds and analyzed the native structure of SaThiM and complexes with the natural substrate 5-(hydroxyethyl)-4-methylthiazole (THZ) and two selected substrate analogues.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms ...diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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.pdbx_dist_value / _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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydroxyethylthiazole kinase
B: Hydroxyethylthiazole kinase
C: Hydroxyethylthiazole kinase
E: Hydroxyethylthiazole kinase
F: Hydroxyethylthiazole kinase
H: Hydroxyethylthiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,92316
Polymers178,9676
Non-polymers95610
Water6,684371
1
A: Hydroxyethylthiazole kinase
B: Hydroxyethylthiazole kinase
C: Hydroxyethylthiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9869
Polymers89,4833
Non-polymers5036
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-52 kcal/mol
Surface area27170 Å2
MethodPISA
2
E: Hydroxyethylthiazole kinase
F: Hydroxyethylthiazole kinase
H: Hydroxyethylthiazole kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9377
Polymers89,4833
Non-polymers4544
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-38 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.549, 62.741, 108.459
Angle α, β, γ (deg.)92.18, 91.44, 101.32
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23E
14A
24F
15A
25H
16B
26C
17B
27E
18B
28F
19B
29H
110C
210E
111C
211F
112C
212H
113E
213F
114E
214H
115F
215H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLNGLNAA1 - 2601 - 260
21METMETGLNGLNBB1 - 2601 - 260
12METMETGLUGLUAA1 - 2611 - 261
22METMETGLUGLUCC1 - 2611 - 261
13ASNASNGLUGLUAA2 - 2642 - 264
23ASNASNGLUGLUED2 - 2642 - 264
14ASNASNARGARGAA2 - 2562 - 256
24ASNASNARGARGFE2 - 2562 - 256
15METMETILEILEAA1 - 2571 - 257
25METMETILEILEHF1 - 2571 - 257
16METMETGLNGLNBB1 - 2601 - 260
26METMETGLNGLNCC1 - 2601 - 260
17ASNASNGLNGLNBB2 - 2602 - 260
27ASNASNGLNGLNED2 - 2602 - 260
18ASNASNARGARGBB2 - 2562 - 256
28ASNASNARGARGFE2 - 2562 - 256
19METMETILEILEBB1 - 2571 - 257
29METMETILEILEHF1 - 2571 - 257
110ASNASNGLUGLUCC2 - 2612 - 261
210ASNASNGLUGLUED2 - 2612 - 261
111ASNASNARGARGCC2 - 2562 - 256
211ASNASNARGARGFE2 - 2562 - 256
112METMETILEILECC1 - 2571 - 257
212METMETILEILEHF1 - 2571 - 257
113ASNASNARGARGED2 - 2562 - 256
213ASNASNARGARGFE2 - 2562 - 256
114ASNASNILEILEED2 - 2572 - 257
214ASNASNILEILEHF2 - 2572 - 257
115ASNASNARGARGFE2 - 2562 - 256
215ASNASNARGARGHF2 - 2562 - 256

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Hydroxyethylthiazole kinase / / 4-methyl-5-beta-hydroxyethylthiazole kinase / Thz kinase


Mass: 29827.801 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: thiM, SAR2181 / Plasmid: pASK-IBA3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GEY3, hydroxyethylthiazole kinase
#2: Chemical
ChemComp-TZE / 2-(4-METHYL-THIAZOL-5-YL)-ETHANOL / 4-METHYL-5-HYDROXYETHYLTHIAZOLE


Mass: 143.207 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H9NOS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, sitting drop
Details: 18 - 22 % PEG 3,350 (w/v), 0.2 M magnesium formate, 5 % isopropanol (v/v), soaked with 0.5 mM 2-(4-methyl-1,3-thiazol-5-yl)ethanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 119565 / % possible obs: 94.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 21.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementResolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.743 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20951 6189 5 %RANDOM
Rwork0.18615 ---
obs0.18729 117078 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.845 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0.23 Å2-1.79 Å2
2---1.97 Å2-2.1 Å2
3---1.77 Å2
Refinement stepCycle: 1 / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11149 0 58 371 11578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01911063
X-RAY DIFFRACTIONr_bond_other_d0.0090.0210845
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.98115051
X-RAY DIFFRACTIONr_angle_other_deg1.395324802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56551465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.03526.165425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.555151768
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3711531
X-RAY DIFFRACTIONr_chiral_restr0.1010.21848
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112703
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022278
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_it1.2821.0135908
X-RAY DIFFRACTIONr_mcbond_other1.2821.0135907
X-RAY DIFFRACTIONr_mcangle_it2.0611.5077363
X-RAY DIFFRACTIONr_mcangle_other2.051.5047358
X-RAY DIFFRACTIONr_scbond_it1.7411.1945155
X-RAY DIFFRACTIONr_scbond_other1.7411.1945156
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6551.7067689
X-RAY DIFFRACTIONr_long_range_B_refined5.2128.3912103
X-RAY DIFFRACTIONr_long_range_B_other5.1848.21711960
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A150130.07
12B150130.07
21A148910.08
22C148910.08
31A147020.09
32E147020.09
41A130380.08
42F130380.08
51A140220.07
52H140220.07
61B151330.07
62C151330.07
71B145280.09
72E145280.09
81B132180.08
82F132180.08
91B142460.06
92H142460.06
101C146240.09
102E146240.09
111C131180.08
112F131180.08
121C142120.07
122H142120.07
131E130800.09
132F130800.09
141E139440.07
142H139440.07
151F130270.08
152H130270.08
LS refinement shellResolution: 1.905→1.954 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 409 -
Rwork0.285 8039 -
obs--91.14 %
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)
10.8332-0.004-0.11511.1212-0.03921.5940.02780.1706-0.0958-0.3424-0.03140.16440.0216-0.07340.00350.16320.0002-0.00080.20340.06580.1721-14.049-27.12211.519
21.00560.07570.01111.9799-0.5320.758-0.0102-0.09240.17030.023-0.00560.0893-0.1091-0.03340.01570.033-0.00560.0250.1830.08580.1973-17.9110.28629.532
31.6670.163-0.10311.1469-0.08340.8682-0.01740.0124-0.05650.00940.0378-0.25610.07830.152-0.02050.0196-0.01090.01590.24150.06960.20229.074-17.77932.959
41.07820.58541.25762.26841.16611.9965-0.14870.10360.0401-0.1493-0.00540.1943-0.2341-0.01150.15420.3580.0139-0.03750.43590.00070.2621.8837.006-41.484
52.84880.546-0.50272.3510.51852.13340.168-0.3423-0.1890.7126-0.20540.04020.1554-0.16560.03730.5657-0.08030.02970.37140.07830.29367.9464.863-9.791
61.6444-0.21850.41293.62010.80481.2134-0.17840.17730.2584-0.2538-0.050.043-0.42510.0260.22830.537-0.0131-0.1290.31020.03110.310413.15432.833-24.19
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 265
2X-RAY DIFFRACTION2B1 - 262
3X-RAY DIFFRACTION3C1 - 262
4X-RAY DIFFRACTION4E2 - 266
5X-RAY DIFFRACTION5F2 - 257
6X-RAY DIFFRACTION6H1 - 259

+
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