[English] 日本語
Yorodumi
- PDB-5j34: Isopropylmalate dehydrogenase K232M mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j34
TitleIsopropylmalate dehydrogenase K232M mutant
Components3-isopropylmalate dehydrogenase 2, chloroplastic
KeywordsOXIDOREDUCTASE / dehydrogenase / leucine biosynthesis / glucosinolate biosynthesis
Function / homology
Function and homology information


embryo sac development / 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / pollen development / leucine biosynthetic process / chloroplast envelope / chloroplast stroma / plastid / NAD+ binding / chloroplast ...embryo sac development / 3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / pollen development / leucine biosynthetic process / chloroplast envelope / chloroplast stroma / plastid / NAD+ binding / chloroplast / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-isopropylmalate dehydrogenase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.827 Å
AuthorsLee, S.G. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS.
Authors: Lee, S.G. / Nwumeh, R. / Jez, J.M.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-isopropylmalate dehydrogenase 2, chloroplastic
B: 3-isopropylmalate dehydrogenase 2, chloroplastic
C: 3-isopropylmalate dehydrogenase 2, chloroplastic
D: 3-isopropylmalate dehydrogenase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,36414
Polymers173,6914
Non-polymers67410
Water26,2301456
1
A: 3-isopropylmalate dehydrogenase 2, chloroplastic
C: 3-isopropylmalate dehydrogenase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2788
Polymers86,8452
Non-polymers4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-105 kcal/mol
Surface area27040 Å2
MethodPISA
2
B: 3-isopropylmalate dehydrogenase 2, chloroplastic
D: 3-isopropylmalate dehydrogenase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0866
Polymers86,8452
Non-polymers2414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-76 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.803, 76.820, 209.497
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3-isopropylmalate dehydrogenase 2, chloroplastic / / IMDH 2 / Beta-IPM dehydrogenase 2


Mass: 43422.684 Da / Num. of mol.: 4 / Mutation: K232M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IMDH2, IMDH, At1g80560, T21F11.11 / Production host: Escherichia coli (E. coli)
References: UniProt: P93832, 3-isopropylmalate dehydrogenase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1456 / 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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.16 M ammonium sulfate, 0.07 M sodium acetate, 17.5% (v/v) PEG-4000, and 20% (v/v) glycerol
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→38.5 Å / Num. obs: 211778 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.089 / Net I/σ(I): 28.6
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: R8W

Resolution: 1.827→38.41 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.23
RfactorNum. reflection% reflection
Rfree0.1855 10619 5.02 %
Rwork0.1654 --
obs0.1664 211554 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.827→38.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10832 0 34 1456 12322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711283
X-RAY DIFFRACTIONf_angle_d0.99615333
X-RAY DIFFRACTIONf_dihedral_angle_d12.5744276
X-RAY DIFFRACTIONf_chiral_restr0.0431772
X-RAY DIFFRACTIONf_plane_restr0.0052016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8269-1.84770.35142800.31565116X-RAY DIFFRACTION76
1.8477-1.86940.30813330.28386846X-RAY DIFFRACTION99
1.8694-1.89220.29713350.27236679X-RAY DIFFRACTION99
1.8922-1.91610.29813600.26196806X-RAY DIFFRACTION100
1.9161-1.94140.2973480.24916773X-RAY DIFFRACTION99
1.9414-1.9680.24223850.22336812X-RAY DIFFRACTION100
1.968-1.99610.24583640.21156732X-RAY DIFFRACTION100
1.9961-2.02590.23313450.21116808X-RAY DIFFRACTION100
2.0259-2.05750.25823370.20856796X-RAY DIFFRACTION100
2.0575-2.09120.23483720.20346802X-RAY DIFFRACTION100
2.0912-2.12730.22773790.20046816X-RAY DIFFRACTION100
2.1273-2.1660.21723620.18776771X-RAY DIFFRACTION100
2.166-2.20760.19683730.18186811X-RAY DIFFRACTION100
2.2076-2.25270.20833300.17646834X-RAY DIFFRACTION100
2.2527-2.30170.19943710.17226747X-RAY DIFFRACTION100
2.3017-2.35520.18423960.16896808X-RAY DIFFRACTION100
2.3552-2.41410.18793410.1696851X-RAY DIFFRACTION100
2.4141-2.47940.20413390.16816855X-RAY DIFFRACTION100
2.4794-2.55230.19213570.16356778X-RAY DIFFRACTION100
2.5523-2.63470.18183680.16716822X-RAY DIFFRACTION100
2.6347-2.72880.17743770.15896800X-RAY DIFFRACTION100
2.7288-2.8380.17293680.16016786X-RAY DIFFRACTION100
2.838-2.96710.18853630.15916847X-RAY DIFFRACTION100
2.9671-3.12350.19343570.15746803X-RAY DIFFRACTION100
3.1235-3.31910.16593840.1486768X-RAY DIFFRACTION99
3.3191-3.57520.15223590.14886745X-RAY DIFFRACTION98
3.5752-3.93470.16043570.14036591X-RAY DIFFRACTION96
3.9347-4.50330.14483390.13336321X-RAY DIFFRACTION91
4.5033-5.67070.16363110.14596584X-RAY DIFFRACTION95
5.6707-38.41850.18823290.17356427X-RAY DIFFRACTION90
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.5939-0.8035-0.96323.5443-0.20012.158-0.1464-0.1237-0.29510.1693-0.05530.12430.2816-0.13830.17530.3005-0.00980.09840.30280.00690.199624.82269.768851.0316
21.36680.0430.11951.29080.03551.9978-0.0277-0.08380.04850.0692-0.0584-0.0063-0.08980.08030.07690.17570.02080.00240.1979-0.00270.186640.1423.6134.7666
32.8025-1.3437-0.66623.31150.90942.8446-0.1371-0.42-0.40060.2447-0.0689-0.21120.53210.31630.17650.32160.06450.05330.33250.11310.30840.31873.343748.6376
44.27650.81730.92663.6942-0.19821.7615-0.11460.10460.2584-0.1599-0.05910.1673-0.2679-0.14010.18160.28470.0207-0.06910.30520.00230.187163.166828.829353.9017
51.3290.0526-0.07561.21260.02281.9305-0.02290.0924-0.0449-0.0779-0.0607-0.02050.07410.10880.08220.1738-0.01810.0150.19820.00130.190278.684814.884570.0303
62.56011.16580.57253.15440.76042.8092-0.13560.42620.4084-0.3185-0.066-0.1884-0.560.30150.15060.3284-0.0618-0.03820.33530.11730.311978.621535.121956.208
72.8822-0.3376-0.16333.5204-1.48411.5518-0.02970.20020.1387-0.1721-0.1439-0.2427-0.10180.22710.14340.3077-0.00110.0050.28550.05390.199947.022631.3962.1064
81.2786-0.02760.0131.33950.24691.9634-0.05870.0615-0.0221-0.0787-0.02260.07540.0943-0.08290.08320.19650.02110.01270.1732-0.00520.190433.739616.962318.1301
93.1045-1.35430.60442.5424-0.62342.6129-0.04220.315-0.161-0.392-0.18-0.41430.35990.57140.15330.35110.0680.12380.32190.04890.326554.40117.17273.8725
103.62780.84160.01265.0375-0.56982.3602-0.0603-0.1805-0.1420.2132-0.1419-0.25290.09220.28090.20860.30580.0118-0.00990.30070.09650.197386.97456.1077104.4094
111.1381-0.0449-0.03321.14510.05371.8976-0.056-0.06740.0110.0938-0.01390.052-0.0616-0.05230.070.1917-0.02370.01440.177-0.00710.191572.752420.179987.7107
123.1311.1617-0.71592.8515-0.66472.9191-0.0861-0.25680.17440.4018-0.1417-0.416-0.31550.55520.150.3201-0.0645-0.10590.31550.04990.316192.515521.2883100.9173
13222222-2.1472-3.58339.99511.3205-1.5416-8.6078-4.05697.56043.70821.0104-0.1812-0.1050.83470.0371.074797.533830.6614114.3596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 140 through 298 )
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 399 )
4X-RAY DIFFRACTION4chain 'B' and (resid 41 through 139 )
5X-RAY DIFFRACTION5chain 'B' and (resid 140 through 298 )
6X-RAY DIFFRACTION6chain 'B' and (resid 299 through 399 )
7X-RAY DIFFRACTION7chain 'C' and (resid 41 through 149 )
8X-RAY DIFFRACTION8chain 'C' and (resid 150 through 298 )
9X-RAY DIFFRACTION9chain 'C' and (resid 299 through 399 )
10X-RAY DIFFRACTION10chain 'D' and (resid 41 through 127 )
11X-RAY DIFFRACTION11chain 'D' and (resid 128 through 298 )
12X-RAY DIFFRACTION12chain 'D' and (resid 299 through 398 )
13X-RAY DIFFRACTION13chain 'D' and (resid 399 through 399 )

+
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