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- PDB-1zix: Crystal Structure Analysis of the dienelactone hydrolase mutant (... -

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Basic information

Entry
Database: PDB / ID: 1zix
TitleCrystal Structure Analysis of the dienelactone hydrolase mutant (E36D, R105H, C123S, G211D, K234N)- 1.8 A
ComponentsCarboxymethylenebutenolidase
KeywordsHYDROLASE / alpha and beta proteins / 3-D structure / Serine esterase / Aromatic hydrocarbons catabolism
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 putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, H.-K. / Liu, J.-W. / Carr, P.D. / Ollis, D.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase.
Authors: Kim, H.K. / Liu, J.W. / Carr, P.D. / Ollis, D.L.
History
DepositionApr 27, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Sep 28, 2016Group: Other
Revision 1.4Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.5Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxymethylenebutenolidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7824
Polymers25,5061
Non-polymers2763
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.459, 70.823, 77.414
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 Carboxymethylenebutenolidase / Dienelactone hydrolase


Mass: 25505.633 Da / Num. of mol.: 1 / Mutation: E36D, R105H, C123S, G211D, K234N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: clcD / Plasmid: pCY76 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P0A114, carboxymethylenebutenolidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.63 % / Description: the file contains Friedel pairs.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium Citrate buffer, 1.2M Ammonium Sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 12, 2002 / Details: confocal mirrors
RadiationMonochromator: Osmic MaxxFlux Confocal optics (green) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→34 Å / Num. all: 47736 / Num. obs: 46300 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.8
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.194 / Num. unique all: 3985 / % possible all: 95.5

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DIN

1din


Resolution: 1.8→24.25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1154046.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2334 5 %RANDOM
Rwork0.174 ---
obs0.174 46300 96.9 %-
all-47736 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.9339 Å2 / ksol: 0.406609 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---1.15 Å20 Å2
3---1.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 18 158 1954
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.034
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_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.8-1.910.1993885.10.18171830.01757194.7
1.91-2.060.2083830.167756695.5
2.06-2.270.2043780.162770496.4
2.27-2.60.2013930.162772397.4
2.6-3.270.1964000.178782698.5
3.27-340.1913920.189790999.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol_G4.paramgol_G4.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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