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- PDB-4p92: Crystal structure of dienelactone hydrolase C123S mutant at 1.65 ... -

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Basic information

Entry
Database: PDB / ID: 4p92
TitleCrystal structure of dienelactone hydrolase C123S mutant at 1.65 A resolution
ComponentsCarboxymethylenebutenolidase
KeywordsHYDROLASE / Dienelactone hydrolase / a/b hydrolase fold
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: 1.65 Å
AuthorsPorter, J.L. / Carr, P.D. / Collyer, C.A. / Ollis, D.L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing.
Authors: Porter, J.L. / Carr, P.D. / Collyer, C.A. / Ollis, D.L.
History
DepositionApr 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Dec 10, 2014Group: Data collection
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)25,7844
Polymers25,4961
Non-polymers2883
Water4,432246
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint-35 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.230, 70.980, 77.460
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: 25495.746 Da / Num. of mol.: 1 / Mutation: C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: clcD / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P0A114, carboxymethylenebutenolidase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: Ammonium sulfate, sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 22, 2012
RadiationMonochromator: mutilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→77.46 Å / Num. obs: 31176 / % possible obs: 95.6 % / Redundancy: 7.23 % / Net I/σ(I): 50.57
Reflection shellResolution: 1.65→1.7 Å / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZI6

1zi6


Resolution: 1.65→77.46 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.161 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 1578 5.1 %RANDOM
Rwork0.15767 ---
obs0.15841 29557 95.59 %-
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: 10.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.65→77.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1766 0 15 246 2027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021836
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9532505
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.265236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01624.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.481159
X-RAY DIFFRACTIONr_chiral_restr0.0920.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0211443
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: 1.652→1.695 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 98 -
Rwork0.145 1894 -
obs--90.3 %

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