[English] 日本語
Yorodumi
- PDB-1xgv: Isocitrate Dehydrogenase from the hyperthermophile Aeropyrum pernix -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xgv
TitleIsocitrate Dehydrogenase from the hyperthermophile Aeropyrum pernix
ComponentsIsocitrate dehydrogenase
KeywordsOXIDOREDUCTASE / Native enzyme / disulphide-bond
Function / homology
Function and homology information


isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / glyoxylate cycle / tricarboxylic acid cycle / NAD binding / magnesium ion binding
Similarity search - Function
Isocitrate dehydrogenase NADP-dependent, dimeric, prokaryotic / 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
isocitrate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarlstrom, M. / Stokke, R. / Steen, I.H. / Birkeland, N.-K. / Ladenstein, R.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Isocitrate dehydrogenase from the hyperthermophile Aeropyrum pernix: X-ray structure analysis of a ternary enzyme-substrate complex and thermal stability
Authors: Karlstrom, M. / Stokke, R. / Steen, I.H. / Birkeland, N.-K. / Ladenstein, R.
History
DepositionSep 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isocitrate dehydrogenase
B: Isocitrate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)95,9662
Polymers95,9662
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-41 kcal/mol
Surface area33810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.569, 107.569, 171.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRARGARG2AA132 - 257132 - 257
21TYRTYRARGARG2BB132 - 257132 - 257
32ILEILELEULEU2AA279 - 320279 - 320
42ILEILELEULEU2BB279 - 320279 - 320
53VALVALGLYGLY5AA321 - 432321 - 432
63VALVALGLYGLY5BB321 - 432321 - 432
74PROPROLEULEU5AA7 - 1317 - 131
84PROPROLEULEU5BB7 - 1317 - 131

-
Components

#1: Protein Isocitrate dehydrogenase /


Mass: 47982.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: BAA79665 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)
References: UniProt: Q9YE81, isocitrate dehydrogenase (NADP+)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 6K, Magnesium chloride, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9089 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 24, 2003
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9089 Å / Relative weight: 1
ReflectionResolution: 2.2→39.84 Å / Num. all: 51805 / Num. obs: 51735 / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.97
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.91 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ICD

3icd


Resolution: 2.2→39.84 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.778 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25059 2606 5.1 %RANDOM
Rwork0.22479 ---
obs0.22609 48984 99.87 %-
all-51590 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.407 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20 Å2
2---0.65 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6595 0 0 162 6757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216667
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9619053
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755847
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.23284
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2332
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4151.54212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.76126760
X-RAY DIFFRACTIONr_scbond_it1.55332455
X-RAY DIFFRACTIONr_scangle_it2.4274.52293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
672tight positional0.060.05
1619medium positional0.430.5
743loose positional0.675
672tight thermal0.130.5
1619medium thermal0.662
743loose thermal1.610
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 176
Rwork0.252 3552
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.28760.5902-0.23584.0872-0.30461.92820.0397-0.2773-0.25740.3405-0.0549-0.00410.0973-0.00370.01520.0676-0.0021-0.02480.2131-0.00660.0094151.356192.7182-138.4159
22.97061.9512-0.74072.7796-0.49411.9684-0.0184-0.00420.2452-0.0756-0.05130.4689-0.2204-0.2130.06970.04960.0397-0.03430.1393-0.03610.1561128.624993.0646-156.6432
31.61350.7965-0.60343.52780.45392.799-0.00810.06610.0963-0.31930.05420.0273-0.36230.0624-0.0460.11-0.0155-0.01330.1506-0.04380.0358153.3916104.8305-152.5179
45.4813.16911.47239.2166-2.35334.066-0.49421.10070.0297-1.60141.01721.93850.4834-0.2139-0.5230.6287-0.2458-0.4290.75120.11140.7595116.286282.4666-191.7603
52.70071.1075-1.33871.4906-0.16731.7624-0.38310.3261-0.4778-0.35910.0848-0.14420.0961-0.06760.29830.16-0.0460.030.2109-0.0850.1856137.188180.5118-171.3408
64.12832.8457-1.383611.7412-3.99944.8201-0.42811.21360.6583-0.91960.66640.7734-0.4981-0.2173-0.23840.5894-0.154-0.27610.7420.25110.3956127.616297.582-190.4098
70.71540.37210.14781.22290.32330.6145-0.0267-0.0284-0.01310.03770.04150.0181-0.04030.0841-0.01480.151-0.00230.00770.2011-0.02540.1134147.791295.8119-149.6071
82.07651.107-0.46610.5023-0.3340.396-0.19620.1293-0.1251-0.19440.08810.00330.00050.0190.10810.278-0.0420.06390.2997-0.01480.2428132.754781.8688-167.0641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 131
2X-RAY DIFFRACTION2A132 - 321
3X-RAY DIFFRACTION3A322 - 435
4X-RAY DIFFRACTION4B7 - 131
5X-RAY DIFFRACTION5B132 - 321
6X-RAY DIFFRACTION6B322 - 432
7X-RAY DIFFRACTION7A436 - 557
8X-RAY DIFFRACTION8B436 - 472

+
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