[English] 日本語
Yorodumi
- PDB-2qfy: Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qfy
TitleCrystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate dehydrogenase in complex with a-ketoglutarate
ComponentsIsocitrate dehydrogenase [NADP]
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


NADPH regeneration / Peroxisomal protein import / glutamate biosynthetic process / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / glyoxylate cycle / mitochondrial nucleoid / tricarboxylic acid cycle ...NADPH regeneration / Peroxisomal protein import / glutamate biosynthetic process / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / NADP metabolic process / glyoxylate cycle / mitochondrial nucleoid / tricarboxylic acid cycle / Neutrophil degranulation / peroxisome / NAD binding / magnesium ion binding / mitochondrion / cytosol
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / Isocitrate dehydrogenase [NADP], mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPeng, Y.J. / Ding, J.P.
CitationJournal: Protein Sci. / Year: 2008
Title: Structural studies of Saccharomyces cerevesiae mitochondrial NADP-dependent isocitrate dehydrogenase in different enzymatic states reveal substantial conformational changes during the catalytic reaction
Authors: Peng, Y.J. / Zhong, C. / Huang, W. / Ding, J.P.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
E: Isocitrate dehydrogenase [NADP]
F: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,73512
Polymers288,8596
Non-polymers8776
Water24,7351373
1
A: Isocitrate dehydrogenase [NADP]
B: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5784
Polymers96,2862
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-49 kcal/mol
Surface area32640 Å2
MethodPISA
2
C: Isocitrate dehydrogenase [NADP]
D: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5784
Polymers96,2862
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-46 kcal/mol
Surface area32720 Å2
MethodPISA
3
E: Isocitrate dehydrogenase [NADP]
F: Isocitrate dehydrogenase [NADP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5784
Polymers96,2862
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-47 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.900, 98.480, 190.600
Angle α, β, γ (deg.)90.000, 98.400, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Isocitrate dehydrogenase [NADP] / Idp1p / Oxalosuccinate decarboxylase / IDH / NADP+ / -specific ICDH / IDP


Mass: 48143.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: YPH499 / Gene: IDP1 / Plasmid: pET-3E-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS
References: UniProt: P21954, isocitrate dehydrogenase (NADP+)
#2: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1373 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M HEPES-Na, 0.2M Li2SO4, 0.1M NaF, 20% PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2005 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 160580 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 39.8 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.074 / Χ2: 1.232 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.1 / Num. unique all: 16016 / Rsym value: 0.276 / Χ2: 0.547 / % possible all: 99.7

-
Phasing

Phasing MRCor.coef. Fo:Fc: 0.684 / Packing: 0.593
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation4 Å10 Ågeneral97.2 2

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFW

2qfw


Resolution: 2.1→43.65 Å / Rfactor Rfree error: 0.003 / FOM work R set: 0.818 / Data cutoff high absF: 2373589.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 7797 4.9 %RANDOM
Rwork0.206 ---
obs-158401 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.246 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å20 Å2-11.25 Å2
2--1.04 Å20 Å2
3----4.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19527 0 60 1373 20960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.1-2.110.3311730.30129493122
2.11-2.130.331420.28230523194
2.13-2.140.291530.2730563209
2.14-2.160.2991700.26929633133
2.16-2.180.3511560.26829833139
2.18-2.190.2811720.24930493221
2.19-2.210.2551530.23330533206
2.21-2.230.2631510.22929343085
2.23-2.240.3341720.2530133185
2.24-2.260.2891520.2530353187
2.26-2.280.321710.23730173188
2.28-2.30.2851420.24529913133
2.3-2.320.3511540.28630303184
2.32-2.340.2811380.25830733211
2.34-2.370.2811640.22829903154
2.37-2.390.2771450.22330463191
2.39-2.410.2611340.22330653199
2.41-2.440.2931610.23329863147
2.44-2.460.3081660.23130073173
2.46-2.490.2781650.22330533218
2.49-2.520.2841490.2230193168
2.52-2.550.2441510.20729963147
2.55-2.580.2591580.20830903248
2.58-2.610.2841550.22429803135
2.61-2.650.291650.22730343199
2.65-2.680.2281540.21630633217
2.68-2.720.2781670.21629813148
2.72-2.760.2481670.21930493216
2.76-2.80.2641570.21330333190
2.8-2.850.2781540.22430263180
2.85-2.90.2811610.22430603221
2.9-2.950.2591400.22730243164
2.95-3.010.2741690.23430303199
3.01-3.070.2541510.20830503201
3.07-3.140.2681520.22130083160
3.14-3.210.2421360.21930393175
3.21-3.290.2781400.22430963236
3.29-3.380.281480.21630383186
3.38-3.480.2681740.22129893163
3.48-3.590.2941380.21930783216
3.59-3.720.2261670.20229973164
3.72-3.870.2291570.18930153172
3.87-4.040.2071540.17929903144
4.04-4.260.191680.17229953163
4.26-4.520.2021510.15729593110
4.52-4.870.2021610.16129863147
4.87-5.360.2241770.17930093186
5.36-6.140.2221570.19830623219
6.14-7.730.2331510.19630583209
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3akg.paramakg.top

+
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://pdbjlvh1.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