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- PDB-1zj5: Crystal Structure Analysis of the dienelactone hydrolase mutant (... -

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Basic information

Entry
Database: PDB / ID: 1zj5
TitleCrystal Structure Analysis of the dienelactone hydrolase mutant (E36D, C123S, A134S, S208G, A229V, K234R) bound with the PMS moiety of the protease inhibitor, Phenylmethylsulfonyl fluoride (PMSF)- 1.7 A
ComponentsCarboxymethylenebutenolidase
KeywordsHYDROLASE / alpha and beta proteins / 3-D structure / Serine esterase / Aromatic hydrocarbons catabolism / PMSF
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: 1.7 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 28, 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_conn ...database_2 / 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 1.5Oct 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)25,9624
Polymers25,6781
Non-polymers2843
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.549, 70.658, 77.627
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: 25677.947 Da / Num. of mol.: 1 / Mutation: E36D, C123S, A134S, S208G, A229V, K234R
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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.42 Å3/Da / Density % sol: 48.71 % / 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: Jul 22, 2003 / Details: confocal mirrors
RadiationMonochromator: Osmic MaxFlux 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→15 Å / Num. all: 55487 / Num. obs: 54785 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.7
Reflection shellResolution: 1.7→1.81 Å / Rmerge(I) obs: 0.204 / Num. unique all: 4635 / % possible all: 96.7

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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→14.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1047938.07 / 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
Rfree0.21 2727 5 %RANDOM
Rwork0.184 ---
obs0.184 54785 98.6 %-
all-55487 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 17.4062 Å2 / ksol: 0.407157 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.7→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 16 124 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.025
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_deg2.4
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_d2.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.861.5
X-RAY DIFFRACTIONc_mcangle_it3.582
X-RAY DIFFRACTIONc_scbond_it5.62
X-RAY DIFFRACTIONc_scangle_it7.042.5
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 (%)
1.7-1.810.3124455.20.25281440.015858993
1.81-1.950.224140.176921599.8
1.95-2.140.2224830.1829255100
2.14-2.450.2264640.19924199.8
2.45-3.080.2264750.1839229100
3.08-150.1784460.1799256100
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_G3PM.paramprotein_G3PM.top
X-RAY DIFFRACTION2gol_G3PM.paramgol_G3PM.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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