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- PDB-4u2f: Crystal structure of dienelactone hydrolase B-1 variant (Q35H, F3... -

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Basic information

Entry
Database: PDB / ID: 4u2f
TitleCrystal structure of dienelactone hydrolase B-1 variant (Q35H, F38L, Y64H, Q110L, C123S, Y137C, Y145C, N154D, E199G, S208G and G211D) at 1.80 A resolution
ComponentsCarboxymethylenebutenolidase
KeywordsHYDROLASE / a/b hydrolase fold
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 sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsPorter, J.L. / Collyer, C.A. / Ollis, D.L.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP120104262 Australia
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search.
Authors: Porter, J.L. / Boon, P.L. / Murray, T.P. / Huber, T. / Collyer, C.A. / Ollis, D.L.
History
DepositionJul 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)25,2792
Polymers25,1831
Non-polymers961
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.934, 70.295, 74.264
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 / DLH


Mass: 25182.506 Da / Num. of mol.: 1
Mutation: Q35H, F38L, Y64H, Q110L, C123S, Y137C, Y145C, N154D, E199G, S208G, G211D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: B13 / Gene: clcD / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha] / References: UniProt: P0A115, carboxymethylenebutenolidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→51.05 Å / Num. obs: 27036 / % possible obs: 98.3 % / Redundancy: 6 % / Net I/σ(I): 20.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data scaling
SCALEPACKdata scaling
RefinementResolution: 1.8→51.05 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.944 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21755 1204 5 %RANDOM
Rwork0.19049 ---
obs0.19183 22895 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.339 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.8→51.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 5 173 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191827
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9482496
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1855244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.09323.90282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67515269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9231510
X-RAY DIFFRACTIONr_chiral_restr0.1210.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211441
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 75 -
Rwork0.259 1544 -
obs--100 %

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