[English] 日本語
Yorodumi
- PDB-5z9y: Crystal structure of Mycobacterium tuberculosis thiazole synthase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z9y
TitleCrystal structure of Mycobacterium tuberculosis thiazole synthase (ThiG) complexed with DXP
ComponentsThiazole synthase
KeywordsTRANSFERASE / alpha-beta barrel / covalently bound / carbinolamine intermediate / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


thiazole synthase / thiazole synthase activity / thiamine diphosphate biosynthetic process / cytoplasm
Similarity search - Function
Thiazole synthase / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-DEOXY-D-XYLULOSE-5-PHOSPHATE / Thiazole synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.48 Å
AuthorsZhang, J. / Zhang, B. / Zhao, Y. / Yang, X. / Huang, M. / Cui, P. / Zhang, W. / Li, J. / Zhang, Y.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Snapshots of catalysis: Structure of covalently bound substrate trapped in Mycobacterium tuberculosis thiazole synthase (ThiG).
Authors: Zhang, J. / Zhang, B. / Zhao, Y. / Yang, X. / Huang, M. / Cui, P. / Zhang, W. / Li, J. / Zhang, Y.
History
DepositionFeb 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiazole synthase
B: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1624
Polymers51,7332
Non-polymers4282
Water6,323351
1
A: Thiazole synthase
hetero molecules

A: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1624
Polymers51,7332
Non-polymers4282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area4380 Å2
ΔGint-29 kcal/mol
Surface area17950 Å2
MethodPISA
2
B: Thiazole synthase
hetero molecules

B: Thiazole synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1624
Polymers51,7332
Non-polymers4282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area4680 Å2
ΔGint-28 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.670, 116.670, 123.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Thiazole synthase


Mass: 25866.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: thiG, Rv0417, MTCY22G10.14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WG73, thiazole synthase
#2: Chemical ChemComp-DXP / 1-DEOXY-D-XYLULOSE-5-PHOSPHATE


Mass: 214.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium malonate pH 5.0, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.48→61.66 Å / Num. obs: 82214 / % possible obs: 99.7 % / Redundancy: 36.1 % / Rpim(I) all: 0.014 / Rrim(I) all: 0.088 / Net I/σ(I): 26.2 / Num. measured all: 2970865
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.48-1.5120.41.47913738810.5212.40895.6
4.02-61.7133.990.615247745000.0070.041100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
XDSdata reduction
RefinementResolution: 1.48→58.335 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 4063 4.95 %
Rwork0.1634 78088 -
obs0.1646 82151 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.54 Å2 / Biso mean: 26.6034 Å2 / Biso min: 14.74 Å2
Refinement stepCycle: final / Resolution: 1.48→58.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 26 351 3729
Biso mean--33.97 38.37 -
Num. residues----466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0213428
X-RAY DIFFRACTIONf_angle_d1.8554690
X-RAY DIFFRACTIONf_chiral_restr0.118592
X-RAY DIFFRACTIONf_plane_restr0.01603
X-RAY DIFFRACTIONf_dihedral_angle_d12.211220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.49740.31041130.27492577269096
1.4974-1.51570.25381240.25862589271397
1.5157-1.53490.25461470.24042575272298
1.5349-1.55510.26981470.22652642278999
1.5551-1.57640.23071390.20822642278199
1.5764-1.59890.22351560.199726622818100
1.5989-1.62280.21491530.197926462799100
1.6228-1.64810.21851650.185526302795100
1.6481-1.67520.21671490.178226382787100
1.6752-1.7040.19121320.170526992831100
1.704-1.7350.19411240.169926852809100
1.735-1.76840.16741370.164927012838100
1.7684-1.80450.20271550.157726372792100
1.8045-1.84370.20671420.15426762818100
1.8437-1.88660.17631320.155326862818100
1.8866-1.93380.1831460.151926662812100
1.9338-1.98610.17631480.145726822830100
1.9861-2.04450.19181300.14927192849100
2.0445-2.11050.20151590.152126572816100
2.1105-2.1860.18571310.147727052836100
2.186-2.27350.17521620.151226852847100
2.2735-2.3770.19281380.153227292867100
2.377-2.50230.161270.15827062833100
2.5023-2.65910.20611380.159627462884100
2.6591-2.86440.17251420.165727212863100
2.8644-3.15260.18041180.164527922910100
3.1526-3.60870.18281330.159127752908100
3.6087-4.54640.16871260.151528352961100
4.5464-58.38030.19541500.173629853135100
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)
10.3174-0.0926-0.02920.1170.22030.27490.03670.08770.01560.0031-0.05290.1039-0.0132-0.16630.00010.2114-0.00060.01770.2793-0.01560.211642.2377-22.32446.896
20.16580.06340.00110.2547-0.01660.2925-0.27550.25150.1567-0.66630.06220.1879-0.0082-0.1923-0.03170.23510.0311-0.02750.25790.03690.314441.6423-5.85378.9002
30.31750.00510.19540.56490.03460.4977-0.0566-0.03310.15580.01730.01360.0072-0.1380.027200.2243-0.00890.02490.2179-0.01650.26351.7191-6.569515.9201
40.27560.0437-0.16260.48340.16480.3576-0.0061-0.00390.0137-0.0043-0.00710.0003-0.00820.00960.00010.1939-0.00180.00120.2048-0.01150.179259.901-24.942713.3166
50.0713-0.07310.07780.38940.12940.1796-0.0203-0.02190.15180.16550.091-0.1952-0.14790.00470.00030.26420.0037-0.01410.1951-0.01350.235392.0230.794322.8351
60.5795-0.3340.080.77480.09270.4964-0.0141-0.01290.0354-0.00850.03250.0457-0.0323-0.0118-00.1818-0.00670.01250.1690.00710.191577.6033-1.327418.2316
70.0030.0129-0.00260.0363-0.00350.0048-0.04860.13130.0589-0.3254-0.0866-0.0414-0.0668-0.13340.00050.2333-0.01320.01630.2097-0.01610.225482.5179-24.9356-6.5263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 64 )
2X-RAY DIFFRACTION2chain 'A' and (resid 65 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 245 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 64 )
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 236 )
7X-RAY DIFFRACTION7chain 'B' and (resid 237 through 247 )

+
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