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- PDB-1iup: meta-Cleavage product hydrolase from Pseudomonas fluorescens IP01... -

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Basic information

Entry
Database: PDB / ID: 1iup
Titlemeta-Cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) S103A mutant complexed with isobutyrates
Componentsmeta-Cleavage product hydrolase
KeywordsHYDROLASE / aromatic compounds / cumene / isopropylbenzene / meta-cleavage compound hydrolase / polychlorinated biphenyl degradation / Pseudomonas fluorescens IP01 / alpha/beta-hydrolase / substrate specificity / cumene degradation / PCB / beta-ketolase
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
: / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-METHYL-PROPIONIC ACID / 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFushinobu, S. / Saku, T. / Hidaka, M. / Jun, S.-Y. / Nojiri, H. / Yamane, H. / Shoun, H. / Omori, T. / Wakagi, T.
Citation
Journal: PROTEIN SCI. / Year: 2002
Title: Crystal structures of a meta-cleavage product hydrolase from Pseudomonas fluorescens IP01 (CumD) complexed with cleavage products
Authors: Fushinobu, S. / Saku, T. / Hidaka, M. / Jun, S.-Y. / Nojiri, H. / Yamane, H. / Shoun, H. / Omori, T. / Wakagi, T.
#1: Journal: J.Biosci.Bioeng. / Year: 2002
Title: Purification, characterization, and steady-state kinetics of a meta-cleavage compound hydrolase from Pseudomonas fluorescens IP01
Authors: Saku, T. / Fushinobu, S. / Jun, S.-Y. / Ikeda, N. / Nojiri, H. / Yamane, H. / Omori, T. / Wakagi, T.
#2: Journal: Appl.Environ.Microbiol. / Year: 1996
Title: Analysis of cumene (isopropylbenzene) degradation genes from Pseudomonas fluorescens IP01
Authors: Habe, H. / Kasuga, K. / Nojiri, H. / Yamane, H. / Omori, T.
History
DepositionMar 6, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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 1.4Oct 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

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Assembly

Deposited unit
A: meta-Cleavage product hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7714
Polymers31,5071
Non-polymers2643
Water6,936385
1
A: meta-Cleavage product hydrolase
hetero molecules

A: meta-Cleavage product hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5428
Polymers63,0132
Non-polymers5296
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)77.350, 116.584, 78.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by the two fold axis: -x,y,1/2-z

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Components

#1: Protein meta-Cleavage product hydrolase / 2-hydroxy-6-oxo-7-methylocta-2 / 4-dienoate hydrolase


Mass: 31506.607 Da / Num. of mol.: 1 / Mutation: S103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: IP01 / Gene: cumD / Plasmid: pIP140 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P96965, EC: 3.7.1.9
#2: Chemical ChemComp-ALQ / 2-METHYL-PROPIONIC ACID


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 3.9
Details: PEG4000, ammonium isobutyrate, sodium isobutyrate, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.0 mg/mlprotein1drop
220 %PEG40001reservoir
30.1 Mammonium isobutyrate1reservoir
40.1 Msodium isobutyrate1reservoirpH3.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 26, 2001
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→21.719 Å / Num. all: 47219 / Num. obs: 47219 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 7.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6823 / Rsym value: 0.412 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 187984 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.412

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C4X

1c4x


Resolution: 1.6→21.72 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2358 5 %RANDOM
Rwork0.188 ---
all0.1896 47196 --
obs0.1896 47196 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5603 Å2 / ksol: 0.342979 e/Å3
Displacement parametersBiso mean: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2---0.4 Å20 Å2
3----0.23 Å2
Refine analyzeLuzzati coordinate error free: 0.2 Å / Luzzati sigma a free: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→21.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 18 385 2542
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.81.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it3.322
X-RAY DIFFRACTIONc_scangle_it4.672.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 381 4.9 %
Rwork0.237 7400 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3IBA.PARAMIBA.TOP
Refinement
*PLUS
Highest resolution: 1.6 Å / % reflection Rfree: 5 % / Rfactor obs: 0.189 / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Rfactor Rfree: 0.284 / Rfactor Rwork: 0.237

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