[English] 日本語
Yorodumi
- PDB-6vb9: Covalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lya... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vb9
TitleCovalent adduct of cis-2,3-epoxysuccinic acid with Isocitrate Lyase-1 from Mycobacterium tuberculosis
ComponentsIsocitrate lyase
KeywordsLYASE / enzyme / covalent inhibitor / substrate analog / Structural Genomics / PSI-Biology / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / carboxylic acid metabolic process / glyoxylate cycle / zymogen binding / tricarboxylic acid cycle / cellular response to hypoxia ...methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / carboxylic acid metabolic process / glyoxylate cycle / zymogen binding / tricarboxylic acid cycle / cellular response to hypoxia / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
ACETIC ACID / OXALIC ACID / DI(HYDROXYETHYL)ETHER / Isocitrate lyase / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.881 Å
AuthorsKrieger, I.V. / Pham, T.V. / Meek, T.D. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01A1095208 United States
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: Covalent Inactivation of Mycobacterium tuberculosis Isocitrate Lyase by cis -2,3-Epoxy-Succinic Acid.
Authors: Pham, T.V. / Mellott, D.M. / Moghadamchargari, Z. / Chen, K. / Krieger, I. / Laganowsky, A. / Sacchettini, J.C. / Meek, T.D.
History
DepositionDec 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isocitrate lyase
B: Isocitrate lyase
C: Isocitrate lyase
D: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,47826
Polymers190,1954
Non-polymers1,28322
Water17,493971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34410 Å2
ΔGint-209 kcal/mol
Surface area49110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.065, 129.065, 167.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Isocitrate lyase


Mass: 47548.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Cys 196 is chemically modified by cis-2,3-epoxysuccinic acid
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: aceA_1, aceA, ERS007703_00218, ERS023446_00716, ERS027651_01707, EZX46_15490, FDK60_05445, FDK62_09180, SAMEA2682864_01056, SAMEA2683035_00941
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045H6H0, UniProt: P9WKK7*PLUS, isocitrate lyase

-
Non-polymers , 5 types, 993 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H2O4
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Nonpolymer detailsGOX represents glyoxylate hydrate

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8.0 Sodium Acetate (0.2 M) 30% PEG 4000

-
Data collection

DiffractionMean temperature: 160 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 120374 / % possible obs: 90.7 % / Redundancy: 9 % / Biso Wilson estimate: 24.56 Å2 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.104 / Rrim(I) all: 0.318 / Χ2: 0.559 / Net I/σ(I): 2.2 / Num. measured all: 1087767
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.88-1.914.92.68734940.1311.33.0020.44153.1
1.91-1.955.32.40338820.1961.1172.6620.44859.4
1.95-1.985.62.10143410.280.9382.3110.45666.1
1.98-2.036.11.92647710.3110.8262.1030.45172.5
2.03-2.076.61.65551990.3860.6841.7980.46279.3
2.07-2.127.11.44457680.460.5741.5590.46987.7
2.12-2.177.91.27362420.550.4791.3650.47595.3
2.17-2.239.81.1466170.7120.3831.2050.47999.8
2.23-2.2910.41.02865980.7490.3361.0830.499100
2.29-2.3710.30.87865520.8330.2880.9250.501100
2.37-2.4510.20.76365870.8570.2520.8040.513100
2.45-2.559.60.63566280.8640.2170.6730.51999.8
2.55-2.6710.20.51366130.9220.1690.5410.53799.9
2.67-2.8110.40.43466300.9470.1420.4580.54599.9
2.81-2.9810.10.33466530.9660.1110.3530.592100
2.98-3.219.70.27266040.970.0920.2880.62999.3
3.21-3.5410.40.19866780.9850.0640.2080.68100
3.54-4.05100.1467050.9910.0460.1470.74899.9
4.05-5.110.20.1167930.9940.0360.1160.70999.8
5.1-509.60.08570190.9970.0290.090.59799.5

-
Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8I

1f8i


Resolution: 1.881→48.935 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.94
RfactorNum. reflection% reflection
Rfree0.2276 5913 4.96 %
Rwork0.1789 --
obs0.1813 119322 89.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.82 Å2 / Biso mean: 26.5554 Å2 / Biso min: 9.49 Å2
Refinement stepCycle: final / Resolution: 1.881→48.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13268 0 103 971 14342
Biso mean--35.48 27.73 -
Num. residues----1708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713715
X-RAY DIFFRACTIONf_angle_d0.85318647
X-RAY DIFFRACTIONf_chiral_restr0.0542043
X-RAY DIFFRACTIONf_plane_restr0.0062468
X-RAY DIFFRACTIONf_dihedral_angle_d4.67111043
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8814-1.90280.35391140.3509192646
1.9028-1.92520.38021100.3216211651
1.9252-1.94860.38561220.2951238958
1.9486-1.97330.33561580.2715260163
1.9733-1.99930.30871440.2715283968
1.9993-2.02670.33551470.2717296771
2.0267-2.05560.30451700.2567319777
2.0556-2.08630.30951900.2411342682
2.0863-2.11890.31511680.2334372789
2.1189-2.15360.30551900.2287393594
2.1536-2.19080.27562230.2266410899
2.1908-2.23060.27922290.22024165100
2.2306-2.27350.2962160.21154187100
2.2735-2.31990.28182250.2024122100
2.3199-2.37040.24012160.20084178100
2.3704-2.42550.25172240.2014186100
2.4255-2.48620.23832050.19814194100
2.4862-2.55340.25822140.1964184100
2.5534-2.62850.26152220.1854179100
2.6285-2.71340.23552140.18824198100
2.7134-2.81030.25771950.18384230100
2.8103-2.92280.2482140.18134207100
2.9228-3.05580.20122380.17934175100
3.0558-3.21690.2282020.1844420899
3.2169-3.41840.21462100.174253100
3.4184-3.68230.19852130.15414236100
3.6823-4.05270.182230.14034241100
4.0527-4.63870.18652480.12854257100
4.6387-5.84280.16212500.12994305100
5.8428-48.930.17622190.1428447399

+
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