[English] 日本語
Yorodumi
- PDB-7e3n: Crystal structure of Isocitrate dehydrogenase D252N mutant from T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e3n
TitleCrystal structure of Isocitrate dehydrogenase D252N mutant from Trypanosoma brucei in complexed with NADP+, alpha-ketoglutarate, and ca2+
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / TRYPANOSOMA BRUCEI / GLYCOSOME / METABOLISM / ISOCITRATE DEHYDROGENASE
Function / homology
Function and homology information


isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP+ metabolic process / glycosome / tricarboxylic acid cycle / NAD binding / magnesium ion binding / mitochondrion
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase
Similarity search - Domain/homology
ISOCITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Isocitrate dehydrogenase [NADP]
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArai, N. / Shiba, T. / Inaoka, D.K. / Kita, K. / Wang, X. / Otani, M. / Matsushiro, S. / Kojima, C.
CitationJournal: To Be Published
Title: Crystal structure of Isocitrate dehydrogenase from Trypanosoma brucei.
Authors: Arai, N. / Shiba, T. / Inaoka, D.K. / Kita, K. / Wang, X. / Otani, M. / Matsushiro, S. / Kojima, C.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7664
Polymers46,7911
Non-polymers9763
Water1,56787
1
A: Isocitrate dehydrogenase [NADP]
hetero molecules

A: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5328
Polymers93,5812
Non-polymers1,9516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area10490 Å2
ΔGint-78 kcal/mol
Surface area31230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.267, 89.767, 62.031
Angle α, β, γ (deg.)90.00, 121.04, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

-
Components

#1: Protein Isocitrate dehydrogenase [NADP]


Mass: 46790.605 Da / Num. of mol.: 1 / Mutation: M1S, D252N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb11.03.0230 / Plasmid: PET-SUMO / Production host: Escherichia coli (E. coli)
References: UniProt: Q387G0, isocitrate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 14% PEG6000,100MM HEPES BUFFER / PH range: 7.0-8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→18.94 Å / Num. obs: 39065 / % possible obs: 99.1 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.07 / Net I/σ(I): 14.79
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.61 / Num. unique obs: 6256 / CC1/2: 0.932 / Rrim(I) all: 0.551 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AJA

6aja


Resolution: 1.9→18.94 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.403 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23721 1962 5 %RANDOM
Rwork0.20528 ---
obs0.20687 37060 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→18.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 62 87 3340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193323
X-RAY DIFFRACTIONr_bond_other_d0.0010.023136
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.974500
X-RAY DIFFRACTIONr_angle_other_deg0.83237215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48423.423149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86515576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8521524
X-RAY DIFFRACTIONr_chiral_restr0.0990.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023693
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02772
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_it1.693.2671603
X-RAY DIFFRACTIONr_mcbond_other1.6873.2661602
X-RAY DIFFRACTIONr_mcangle_it2.5094.8932002
X-RAY DIFFRACTIONr_mcangle_other2.5094.8952003
X-RAY DIFFRACTIONr_scbond_it1.9143.4731720
X-RAY DIFFRACTIONr_scbond_other1.9113.4741718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0535.1132498
X-RAY DIFFRACTIONr_long_range_B_refined4.10425.7173770
X-RAY DIFFRACTIONr_long_range_B_other4.10225.7123741
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.944 Å
RfactorNum. reflection% reflection
Rfree0.312 173 -
Rwork0.286 2638 -
obs--97.81 %

+
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