[English] 日本語
Yorodumi
- PDB-1pya: REFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pya
TitleREFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE FROM LACTOBACILLUS 30A
Components(PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)) x 2
KeywordsCARBOXY-LYASE
Function / homology
Function and homology information


histidine decarboxylase / histidine decarboxylase activity / histidine metabolic process
Similarity search - Function
Pyruvoyl-Dependent Histidine Decarboxylas; Chain A / Pyruvoyl-Dependent Histidine Decarboxylas, subunit A / Histidine decarboxylase proenzyme / Histidine decarboxylase proenzyme, N-terminal / Histidine carboxylase PI chain / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich ...Pyruvoyl-Dependent Histidine Decarboxylas; Chain A / Pyruvoyl-Dependent Histidine Decarboxylas, subunit A / Histidine decarboxylase proenzyme / Histidine decarboxylase proenzyme, N-terminal / Histidine carboxylase PI chain / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich / Few Secondary Structures / Irregular / Alpha Beta
Similarity search - Domain/homology
Histidine decarboxylase proenzyme
Similarity search - Component
Biological speciesLactobacillus sp. 30A (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsGallagher, T. / Rozwarski, D.A. / Ernst, S.R. / Hackert, M.L.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a.
Authors: Gallagher, T. / Rozwarski, D.A. / Ernst, S.R. / Hackert, M.L.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Pyruvoyl-Dependent Histidine Decarboxylase: Active Site Structure and Mechanistic Analysis
Authors: Gallagher, T. / Snell, E.E. / Hackert, M.L.
#2: Journal: J.Mol.Biol. / Year: 1985
Title: Structure Determination of Histidine Decarboxylase from Lactobacillus 30A at 3.0 Angstroms Resolution
Authors: Parks, E.H. / Ernst, S.R. / Hamlin, R. / Xuong, N.H. / Hackert, M.L.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: The Molecular Symmetry of Histidine Decarboxylase and Prohistidine Decarboxylase by Rotation Function Analysis
Authors: Parks, E.H. / Clinger, K. / Hackert, M.L.
#4: Journal: J.Biol.Chem. / Year: 1981
Title: Crystallization and Subunit Structure of Histidine Decarboxylase from Lactobacillus 30A
Authors: Hackert, M.L. / Meador, W.E. / Oliver, R.M. / Salmon, J.B. / Rescei, P.A. / Snell, E.E.
History
DepositionDec 18, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_sheet_hbond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Remark 650HELIX ISOLATED TURNS OF A 3-10 HELIX OCCUR AT RESIDUES 98 - 102 AND 266 - 270.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
B: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
C: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
D: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
E: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
F: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)


Theoretical massNumber of molelcules
Total (without water)102,4096
Polymers102,4096
Non-polymers00
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29310 Å2
ΔGint-135 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.700, 221.700, 107.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.47771, -0.503811, -0.7197), (0.515178, -0.502924, 0.694017), (-0.711608, -0.702312, 0.019301)113.89865, 110.27171, 156.94324
2given(0.47771, 0.515178, -0.711608), (-0.503811, -0.502924, -0.702312), (-0.7197, 0.694017, 0.019301)0.46197, 223.06477, 2.41324
DetailsTWO TRIMERS RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS GENERATE THE HEXAMER. THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *C* AND *D*, RESPECTIVELY. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *E* AND *F*, RESPECTIVELY.

-
Components

#1: Protein PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)


Mass: 8850.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. 30A (bacteria) / Strain: 30a / References: UniProt: P00862, histidine decarboxylase
#2: Protein PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)


Mass: 25285.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. 30A (bacteria) / Strain: 30a / References: UniProt: P00862, histidine decarboxylase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal grow
*PLUS
pH: 4.8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-15 mg/mlprotein1drop
20.20 Mammonium acetate1drop
345 %satammonium sulfate1reservoir
40.20 Mammonium acetate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.15 / Rfactor obs: 0.15 / Highest resolution: 2.5 Å
Details: THE SEGMENT NUMBERS ARE AS FOLLOWS: (1,3,5 = BETA SUBUNITS) (2,4,6 = ALPHA SUBUNITS), (7,8,9 = PVL MOIETIES WITH 7-2 REPRESENTING THE PVL GROUP COVALENTLY ATTACHED TO THE BEGINNING OF AN ...Details: THE SEGMENT NUMBERS ARE AS FOLLOWS: (1,3,5 = BETA SUBUNITS) (2,4,6 = ALPHA SUBUNITS), (7,8,9 = PVL MOIETIES WITH 7-2 REPRESENTING THE PVL GROUP COVALENTLY ATTACHED TO THE BEGINNING OF AN ALPHA SUBUNIT OR SEGMENT 2). THE SEGMENT NUMBERS FOR THE THREE *AB* SUBUNITS ARE: 1, 7 - 2; 3, 8 - 4; AND 5, 9 - 6.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8727 0 0 1413 10140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 39926 / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_deg1.3

+
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