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- PDB-1uk6: Crystal structure of a meta-cleavage product hydrolase (CumD) com... -

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Basic information

Entry
Database: PDB / ID: 1uk6
TitleCrystal structure of a meta-cleavage product hydrolase (CumD) complexed with propionate
Components2-hydroxy-6-oxo-7-methylocta-2,4-dienoate 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
PROPANOIC ACID / 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsFushinobu, S. / Jun, S.-Y. / Hidaka, M. / Nojiri, H. / Yamane, H. / Shoun, H. / Omori, T. / Wakagi, T.
CitationJournal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 2005
Title: A Series of Crystal Structures of a meta-Cleavage Product Hydrolase from Pseudomonas fluorescens IP01 (CumD) Complexed with Various Cleavage Products
Authors: Fushinobu, S. / Jun, S.-Y. / Hidaka, M. / Nojiri, H. / Yamane, H. / Shoun, H. / Omori, T. / Wakagi, T.
History
DepositionAug 19, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2004Provider: 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: 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6553
Polymers31,5071
Non-polymers1482
Water6,017334
1
A: 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
hetero molecules

A: 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3106
Polymers63,0132
Non-polymers2964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)76.843, 116.595, 78.537
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, -z.

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Components

#1: Protein 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase / META-CLEAVAGE PRODUCT 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) / 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-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.53 Å3/Da / Density % sol: 51.01 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG4000, AMMONIUM propionate, SODIUM propionate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2002
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→27.46 Å / Num. all: 26055 / Num. obs: 26055 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 5.8 Å2 / Rsym value: 0.115 / Net I/σ(I): 6.3
Reflection shellResolution: 1.95→2.06 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.348 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1IUP

1iup


Resolution: 1.95→27.42 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2243410.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1299 5 %RANDOM
Rwork0.175 ---
all0.177 26055 --
obs0.175 26055 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.2379 Å2 / ksol: 0.337363 e/Å3
Displacement parametersBiso mean: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---0.45 Å20 Å2
3----0.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.95→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 10 334 2483
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_d22.5
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_it1.631.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.362.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 229 5.3 %
Rwork0.201 4056 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PPA.PARAMPPA.TOP

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