[English] 日本語
Yorodumi
- PDB-1dtw: HUMAN BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dtw
TitleHUMAN BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE
Components(BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE ...) x 2
KeywordsOXIDOREDUCTASE / ThDP-binding fold / BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE
Function / homology
Function and homology information


3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / : / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / Glyoxylate metabolism and glycine degradation / carboxy-lyase activity / response to glucocorticoid / response to cAMP / response to nutrient ...3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity / : / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / Glyoxylate metabolism and glycine degradation / carboxy-lyase activity / response to glucocorticoid / response to cAMP / response to nutrient / lipid metabolic process / mitochondrial matrix / protein-containing complex binding / nucleolus / mitochondrion / nucleoplasm / metal ion binding
Similarity search - Function
Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains ...Dehydrogenase, E1 component / Dehydrogenase E1 component / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / THIAMINE DIPHOSPHATE / 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial / 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
Model detailsTHIS IS THE E1 COMPONENT OF AN ALPHA-KETOACID DEHYDROGENASE MULTIENZYME COMPLEX. A NUMBER OF ...THIS IS THE E1 COMPONENT OF AN ALPHA-KETOACID DEHYDROGENASE MULTIENZYME COMPLEX. A NUMBER OF MUTATIONS HAVE BEEN CHARACTERIZED IN THIS ENZYME THAT CAUSE MAPLE SYRUP URINE DISEASE.
AuthorsAEvarsson, A. / Chuang, J.L. / Wynn, R.M. / Turley, S. / Chuang, D.T. / Hol, W.G.J.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease.
Authors: AEvarsson, A. / Chuang, J.L. / Wynn, R.M. / Turley, S. / Chuang, D.T. / Hol, W.G.
History
DepositionJan 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _struct_conn.pdbx_dist_value / _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_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 / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE ALPHA SUBUNIT
B: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0016
Polymers83,4732
Non-polymers5284
Water86548
1
A: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE ALPHA SUBUNIT
B: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE BETA SUBUNIT
hetero molecules

A: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE ALPHA SUBUNIT
B: BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,00212
Polymers166,9474
Non-polymers1,0568
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area26090 Å2
ΔGint-163 kcal/mol
Surface area42900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.760, 143.760, 69.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-366-

HOH

21B-371-

HOH

DetailsThe biological assembly is alpha2beta2 heterotetramer with chains A and B forming one alpha subunit - the other alpha subunit symmetry partner is generated by a two-fold / The biological assembly is alpha2beta2 heterotetramer with chain C forming one beta subunit - the other beta subunit symmetry partner is generated by a two-fold

-
Components

-
BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE ... , 2 types, 2 molecules AB

#1: Protein BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE ALPHA SUBUNIT


Mass: 45571.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: P-HE1-HIS6 / Production host: Escherichia coli (E. coli)
References: UniProt: P12694, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
#2: Protein BRANCHED-CHAIN ALPHA-KETO ACID DEHYDROGENASE BETA SUBUNIT


Mass: 37902.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: P-HE1-HIS6 / Production host: Escherichia coli (E. coli)
References: UniProt: P21953, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)

-
Non-polymers , 4 types, 52 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ethanol, PEG 8000,MES, potassium chloride, magnesium chloride, glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 20K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135-40 %ethanol1reservoir
20-2 %PEG80001reservoir
30.1 MMES1reservoir
418 mg/mlprotein1drop
50.1 MMES1drop
60.25 M1dropKCl
710 %glycerol1drop
81 mMThDP1drop
910 mM1dropMgCl2
101 mMinhibitor1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDetector: CCD / Date: 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 22910 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 49.1 Å2 / Rmerge(I) obs: 0.14
Reflection
*PLUS
Num. obs: 22910 / Num. measured all: 306699

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 2.7→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2036465.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1112 4.9 %RANDOM
Rwork0.224 ---
obs0.224 22858 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.33 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-6.11 Å27.79 Å20 Å2
2--6.11 Å20 Å2
3----12.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 29 48 5670
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it0.111.5
X-RAY DIFFRACTIONc_mcangle_it0.212
X-RAY DIFFRACTIONc_scbond_it0.052
X-RAY DIFFRACTIONc_scangle_it0.112.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 167 4.4 %
Rwork0.304 3612 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2MG-K.PARMG-K.TOP
X-RAY DIFFRACTION3TDP.PARTDP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.375 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.304

+
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