[English] 日本語
Yorodumi
- PDB-7cp1: Crystal structure of isocitrate lyase in complex with succinate a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cp1
TitleCrystal structure of isocitrate lyase in complex with succinate and itaconate
ComponentsIsocitrate lyase
KeywordsLYASE / Glyoxylate cycle / Isocitrate lyase / Succinate / Itaconate / Mycobacterium tuberculosis
Function / homology
Function and homology information


methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle / cellular response to hypoxia / extracellular region ...methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / 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
2-methylidenebutanedioic acid / SUCCINIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsKwon, S. / Park, H.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2017M3A9D8062960
National Research Foundation (NRF, Korea)2018R1A4A1023822 Korea, Republic Of
CitationJournal: Plos One / Year: 2021
Title: Heterogeneous multimeric structure of isocitrate lyase in complex with succinate and itaconate provides novel insights into its inhibitory mechanism.
Authors: Kwon, S. / Chun, H.L. / Ha, H.J. / Lee, S.Y. / Park, H.H.
History
DepositionAug 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Isocitrate lyase
B: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7086
Polymers96,4112
Non-polymers2974
Water11,367631
1
A: Isocitrate lyase
B: Isocitrate lyase
hetero molecules

A: Isocitrate lyase
B: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,41612
Polymers192,8224
Non-polymers5948
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area30000 Å2
ΔGint-185 kcal/mol
Surface area52550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.320, 131.320, 284.882
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-717-

HOH

21B-676-

HOH

31B-726-

HOH

41B-823-

HOH

51B-903-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 2 through 418)
21(chain B and (resid 2 through 192 or (resid 193...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEU(chain A and resid 2 through 418)AA2 - 4182 - 418
21SERSERGLYGLY(chain B and (resid 2 through 192 or (resid 193...BB2 - 1922 - 192
22HISHISLEULEU(chain B and (resid 2 through 192 or (resid 193...BB193 - 194193 - 194
23SERSERLEULEU(chain B and (resid 2 through 192 or (resid 193...BB2 - 4182 - 418
24SERSERLEULEU(chain B and (resid 2 through 192 or (resid 193...BB2 - 4182 - 418
25SERSERLEULEU(chain B and (resid 2 through 192 or (resid 193...BB2 - 4182 - 418
26SERSERLEULEU(chain B and (resid 2 through 192 or (resid 193...BB2 - 4182 - 418
Detailsdimer in the aymmetric unit; tetramer in solution

-
Components

#1: Protein Isocitrate lyase / / ICL / Isocitrase / Isocitratase


Mass: 48205.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Some parts at the ends were not assigned due to poor electron density.
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: icl, Rv0467, MTV038.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WKK7, isocitrate lyase
#2: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ITN / 2-methylidenebutanedioic acid / Itaconic acid


Mass: 130.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.6 M sodium phosphate, 1.2 M potassium phosphate, 0.1 M imidazole (pH 8.5), 250 mM sodium chloride

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9779 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.577→50 Å / Num. obs: 44429 / % possible obs: 95.1 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.043 / Rrim(I) all: 0.158 / Χ2: 0.93 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.58-2.649.40.6728000.8220.1930.7020.92592.4
2.64-2.719.80.5828590.8630.1610.6060.96394
2.71-2.789.70.50329000.8760.1410.5260.97694.9
2.78-2.8610.10.43629360.9060.1190.4561.01496
2.86-2.9510.20.38229340.9230.1040.41.03396.4
2.95-3.069.40.32129850.950.0890.3371.05197
3.06-3.188.70.27529760.960.0810.291.11397.2
3.18-3.3380.20329720.9750.0630.2151.01597.1
3.33-3.57.20.16829840.9820.0570.1790.96396.6
3.5-3.726.70.13329950.9870.050.1430.90896.3
3.72-4.016.80.11430010.990.0450.1230.80796.2
4.01-4.417.70.10829690.9910.0390.1160.81594.7
4.41-5.059.70.09629350.9940.030.1010.86692.9
5.05-6.3615.80.10329600.9960.0250.1060.85192.4
6.36-5025.90.06632230.9990.0130.0680.84893.4

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F8M

1f8m


Resolution: 2.58→43.033 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 2119 4.92 %
Rwork0.1536 40952 -
obs0.1556 43071 92.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.14 Å2 / Biso mean: 32.997 Å2 / Biso min: 15.55 Å2
Refinement stepCycle: final / Resolution: 2.58→43.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 19 641 7102
Biso mean--37.94 36.36 -
Num. residues----832
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2538X-RAY DIFFRACTION3.879TORSIONAL
12B2538X-RAY DIFFRACTION3.879TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.58-2.63740.27931340.228263991
2.6374-2.70330.23211300.206271894
2.7033-2.77640.23111530.2017274995
2.7764-2.85810.28171540.1926277396
2.8581-2.95030.26691430.1863278896
2.9503-3.05570.22561420.1804283597
3.0557-3.1780.27531330.1868285497
3.178-3.32260.19611500.1569281797
3.3226-3.49770.1991420.1513283996
3.4977-3.71670.19951540.142282796
3.7167-4.00350.18311480.1287285096
4.0035-4.40610.16561350.1278281394
4.4061-5.04280.14561510.1214275892
5.0428-6.35010.161070.1356249081
6.3501-43.0330.13211430.1321220269

+
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