[English] 日本語
Yorodumi
- PDB-1din: DIENELACTONE HYDROLASE AT 2.8 ANGSTROMS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1din
TitleDIENELACTONE HYDROLASE AT 2.8 ANGSTROMS
ComponentsDIENELACTONE HYDROLASE
KeywordsHYDROLYTIC ENZYME / DIENELACTONE HYDROLASE / AROMATIC HYDROCARBON CATABOLISM / SERINE ESTERASE / CARBOXYMETHYLENEBUTENOLIDASE
Function / homology
Function and homology information


carboxymethylenebutenolidase / carboxymethylenebutenolidase activity / :
Similarity search - Function
Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Carboxymethylenebutenolidase
Similarity search - Component
Biological speciesPseudomonas knackmussii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsOllis, D.L. / Pathak, D.
Citation
Journal: J.Mol.Biol. / Year: 1990
Title: Refined structure of dienelactone hydrolase at 1.8 A.
Authors: Pathak, D. / Ollis, D.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: X-Ray Crystallographic Structure of Dienelactone Hydrolase at 2.8 A
Authors: Pathak, D. / Ngai, K.L. / Ollis, D.
#2: Journal: J.Biol.Chem. / Year: 1985
Title: Crystallization and Preliminary X-Ray Crystallographic Data of Dienelactone Hydrolase from Pseudomonas Sp. B13
Authors: Ollis, D.L. / Ngai, K.L.
History
DepositionMar 14, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIENELACTONE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)25,5441
Polymers25,5441
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.900, 71.450, 78.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DIENELACTONE HYDROLASE / DLH


Mass: 25543.811 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas knackmussii (bacteria) / Strain: B13 / Gene: CLC D / Plasmid: PDC100 / Gene (production host): CLC D / Production host: Pseudomonas sp. (bacteria)
References: PIR: S02022, UniProt: P0A115*PLUS, carboxymethylenebutenolidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS MICROHETEROGENEITY AT RESIDUE 123. ONE OF THE RESIDUES IS CYSTEINE AND THE OTHER IS ...THERE IS MICROHETEROGENEITY AT RESIDUE 123. ONE OF THE RESIDUES IS CYSTEINE AND THE OTHER IS OXIDIZED CYSTEINE WHICH IS PRESENTED AS RESIDUE CSD. ONLY CSD IS LISTED ON THE SEQRES RECORDS BELOW; BOTH CYS AND CSD ARE LISTED ON SEQADV RECORDS. COORDINATES ARE PRESENTED FOR CYS AND CSD.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.3 / Method: vapor diffusion, hanging drop / Details: Pathak, D., (1988) J.Mol.Biol., 204, 435.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
20.86 M1dropPO4-
31.9 M1reservoirPO4-
1enzyme1drop

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorDetector: AREA DETECTOR / Date: 1987
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 29488 / % possible obs: 95 % / Redundancy: 6 % / Rmerge(I) obs: 0.057

-
Processing

Software
NameClassification
PROLSQrefinement
TNTrefinement
XENGENdata reduction
RefinementResolution: 1.8→10 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.15 --
obs-23835 95 %
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 279 2063
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_deg3.4053
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg22.85715

+
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://pdbjlvh1.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