[English] 日本語
Yorodumi
- PDB-1qpb: PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qpb
TitlePYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE
ComponentsPYRUVATE DECARBOXYLASE (FORM B)
KeywordsLYASE / THIAMINE PYRUVATE / PYRUVAMIDE
Function / homology
Function and homology information


phenylpyruvate decarboxylase / branched-chain-2-oxoacid decarboxylase / phenylpyruvate decarboxylase activity / branched-chain-2-oxoacid decarboxylase activity / indolepyruvate decarboxylase / pyruvate fermentation to ethanol / indolepyruvate decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases ...phenylpyruvate decarboxylase / branched-chain-2-oxoacid decarboxylase / phenylpyruvate decarboxylase activity / branched-chain-2-oxoacid decarboxylase activity / indolepyruvate decarboxylase / pyruvate fermentation to ethanol / indolepyruvate decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / branched-chain amino acid catabolic process / L-tryptophan catabolic process / L-phenylalanine catabolic process / thiamine pyrophosphate binding / magnesium ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Thiamine pyrophosphate (TPP)-dependent enzyme / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding ...: / Thiamine pyrophosphate (TPP)-dependent enzyme / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRUVAMIDE / THIAMINE DIPHOSPHATE / Pyruvate decarboxylase isozyme 1
Similarity search - Component
Biological speciesSACCHAROMYCES PASTORIANUS (lager yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLu, G. / Dobritzsch, D. / Schneider, G.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: The Structural Basis of Substrate Activation in Yeast Pyruvate Decarboxylase a Crystallographic and Kinetic Study
Authors: Lu, G. / Dobritzsch, D. / Baumann, S. / Schneider, G. / Konig, S.
#1: Journal: FEBS Lett. / Year: 1997
Title: Novel Tetramer Assembly of Pyruvate Decarboxylase from Brewer'S Yeast Observed in a New Crystal Form
Authors: Lu, G. / Dobritzsch, D. / Konig, S. / Schneider, G.
History
DepositionNov 26, 1999Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 4, 2000ID: 1YPD
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: DSSP
Remark 700 SHEET DETERMINATION METHOD: DSSP

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PYRUVATE DECARBOXYLASE (FORM B)
B: PYRUVATE DECARBOXYLASE (FORM B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1848
Polymers123,1102
Non-polymers1,0736
Water2,540141
1
A: PYRUVATE DECARBOXYLASE (FORM B)
B: PYRUVATE DECARBOXYLASE (FORM B)
hetero molecules

A: PYRUVATE DECARBOXYLASE (FORM B)
B: PYRUVATE DECARBOXYLASE (FORM B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,36716
Polymers246,2204
Non-polymers2,14712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area19930 Å2
ΔGint-100.8 kcal/mol
Surface area91090 Å2
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-59.81 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.049, 119.700, 81.283
Angle α, β, γ (deg.)90.00, 120.21, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein PYRUVATE DECARBOXYLASE (FORM B) / ALPHA-CARBOXYLASE / PYRUVIC DECARBOXYLASE / ALPHA-KETOACID CARBOXYLASE


Mass: 61555.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FORM B / Source: (natural) SACCHAROMYCES PASTORIANUS (lager yeast) / Strain: WEIHENSTEPHAN 34/70 (2124, BOHEMIAN LAGER) / References: UniProt: P06169, pyruvate decarboxylase
#2: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PYM / PYRUVAMIDE


Mass: 87.077 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 43 %
Crystal growpH: 5.8
Details: 8-14% PEG6000 20MM SODIUM CITRATE AT PH 5.7 1MM DTE, 5MM THDP, 5MM MGSO4
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMsodium citrate1drop
31 mMDTE1drop
45 mMThDP1drop
55 mM1dropMgSO4
6320 mMpyruvamide1drop
720 mMsodium citrate1reservoir
81 mMDTE1reservoir
95 mMThDP1reservoir
105 mM1reservoirMgSO4
1113-14 %PEG60001reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 2, 1997
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 42140 / % possible obs: 88.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 33.0519 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.091 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5 / Rsym value: 0.38 / % possible all: 60
Reflection shell
*PLUS
% possible obs: 56 %

-
Processing

Software
NameVersionClassification
CNS3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PVD

1pvd


Resolution: 2.4→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 15 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION WAS APPLIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1724 4 %RANDOM
Rwork0.233 ---
obs0.233 42411 89 %-
Displacement parametersBiso mean: 31.0519 Å2
Refine analyzeLuzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8550 0 66 141 8757
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.38→2.42 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 25 0.46 %
Rwork0.363 540 -
obs--34.5 %
Software
*PLUS
Name: CNS / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13

+
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