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- PDB-1zic: Crystal Structure Analysis of the dienelactone hydrolase (C123S, ... -

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Basic information

Entry
Database: PDB / ID: 1zic
TitleCrystal Structure Analysis of the dienelactone hydrolase (C123S, R206A) mutant- 1.7 A
ComponentsCarboxymethylenebutenolidase
KeywordsHYDROLASE / alpha and beta proteins / 3-D structure / Serine esterase / Aromatic hydrocarbons / catabolism
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 putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxymethylenebutenolidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6904
Polymers25,4101
Non-polymers2803
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.404, 70.624, 77.275
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: 25409.631 Da / Num. of mol.: 1 / Mutation: C123S, R206A
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.18 % / 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: Mar 21, 2003 / 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: 1.7→14.93 Å / Num. all: 56253 / Num. obs: 52049 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.99 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8
Reflection shellResolution: 1.7→1.81 Å / Rmerge(I) obs: 0.174 / Num. unique all: 4838 / % possible all: 98.4

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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: 1.7→14.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1058480.75 / 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
Rfree0.202 2589 5 %RANDOM
Rwork0.173 ---
obs0.173 52049 92.4 %-
all-56253 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.9144 Å2 / ksol: 0.455972 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 17 184 1971
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.023
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.43
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.641.5
X-RAY DIFFRACTIONc_mcangle_it3.232
X-RAY DIFFRACTIONc_scbond_it4.772
X-RAY DIFFRACTIONc_scangle_it6.142.5
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 (%)
1.7-1.810.24243850.20383810.012881993.8
1.81-1.950.1954270.165902296.3
1.95-2.140.1894460.156890195.1
2.14-2.450.2044560.169878693.7
2.45-3.080.2274370.181856991.7
3.08-150.1933850.18795284.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol_C6.paramgol_C6.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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