[English] 日本語
Yorodumi
- PDB-1dqu: CRYSTAL STRUCTURE OF THE ISOCITRATE LYASE FROM ASPERGILLUS NIDULANS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dqu
TitleCRYSTAL STRUCTURE OF THE ISOCITRATE LYASE FROM ASPERGILLUS NIDULANS
ComponentsISOCITRATE LYASE
KeywordsLYASE / BETA BARREL
Function / homology
Function and homology information


glyoxysome / acetate catabolic process / methylisocitrate lyase / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / carbon utilization / fatty acid catabolic process / glyoxylate cycle / peroxisomal matrix ...glyoxysome / acetate catabolic process / methylisocitrate lyase / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / carbon utilization / fatty acid catabolic process / glyoxylate cycle / peroxisomal matrix / tricarboxylic acid cycle / peroxisome / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #850 / Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Arc Repressor Mutant, subunit A / TIM Barrel ...Arc Repressor Mutant, subunit A - #850 / Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Arc Repressor Mutant, subunit A / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsBritton, K.L. / Langridge, S.J. / Baker, P.J. / Weeradechapon, K. / Sedelnikova, S.E. / De Lucas, J.R. / Rice, D.W. / Turner, G.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: The crystal structure and active site location of isocitrate lyase from the fungus Aspergillus nidulans.
Authors: Britton, K. / Langridge, S. / Baker, P.J. / Weeradechapon, K. / Sedelnikova, S.E. / De Lucas, J.R. / Rice, D.W. / Turner, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Isocitrate Lyase from Aspergillus Nidulans: Crystallization and X-ray Analysis of a Glyoxylate Cycle Enzyme.
Authors: Langridge, S.J. / Baker, P.J. / De Lucas, J.R. / Sedelnikova, S.E. / Turner, G. / Rice, D.W.
History
DepositionJan 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ISOCITRATE LYASE


Theoretical massNumber of molelcules
Total (without water)60,3981
Polymers60,3981
Non-polymers00
Water00
1
A: ISOCITRATE LYASE

A: ISOCITRATE LYASE

A: ISOCITRATE LYASE

A: ISOCITRATE LYASE


Theoretical massNumber of molelcules
Total (without water)241,5934
Polymers241,5934
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area30360 Å2
ΔGint-190 kcal/mol
Surface area75440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.930, 91.930, 152.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe biological assembly is a tetramer constructed from chain A generated by 222 symmetry

-
Components

#1: Protein ISOCITRATE LYASE


Mass: 60398.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Description: MULTICOPY INSERTION OF VECTOR INTO CHROMOSOME / Production host: Emericella nidulans (mold) / References: UniProt: P28298, isocitrate lyase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 2000, sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Langridge, S.J., (1997) Acta Crystallogr., Sect.D, 53, 488.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
21-20 %(w/v)PEG20001drop
30.1 Msodium HEPES1drop

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 27, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 21252 / Num. obs: 21252 / % possible obs: 91.5 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.439 / Num. unique all: 1198 / % possible all: 71.9
Reflection
*PLUS
Num. measured all: 62390

-
Processing

Software
NameVersionClassification
MLPHAREphasing
TNTrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.8→10 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.376 818 -RANDOM
Rwork0.273 ---
all0.276 15857 --
obs0.276 15857 97 %-
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4069 0 0 0 4069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.5
X-RAY DIFFRACTIONt_bond_d0.013
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor all: 0.276
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.5
X-RAY DIFFRACTIONt_planar_d0.011
X-RAY DIFFRACTIONt_plane_restr0.009

+
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