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- PDB-1din: DIENELACTONE HYDROLASE AT 2.8 ANGSTROMS -

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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 / catabolic process
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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY
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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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