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- PDB-2d0d: Crystal Structure of a Meta-cleavage Product Hydrolase (CumD) A12... -

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Basic information

Entry
Database: PDB / ID: 2d0d
TitleCrystal Structure of a Meta-cleavage Product Hydrolase (CumD) A129V Mutant
Components2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
KeywordsHYDROLASE / alpha/beta-hydrolase / beta-ketolase / meta-cleavage product hydrolase / substrate specificity / cumene degradation / polychlorinated biphenyl degradation / PCB
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
PHOSPHATE ION / 2-hydroxy-6-oxo-7-methylocta-2,4-dienoate hydrolase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsJun, S.Y. / Fushinobu, S. / Nojiri, H. / Omori, T. / Shoun, H. / Wakagi, T.
Citation
Journal: Biochim.Biophys.Acta / Year: 2006
Title: Improving the catalytic efficiency of a meta-cleavage product hydrolase (CumD) from Pseudomonas fluorescens IP01
Authors: Jun, S.Y. / Fushinobu, S. / Nojiri, H. / Omori, T. / Shoun, H. / Wakagi, T.
#1: Journal: 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.
#2: 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.
History
DepositionAug 1, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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)31,7764
Polymers31,5511
Non-polymers2253
Water6,702372
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)63,5528
Polymers63,1012
Non-polymers4516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)76.650, 116.623, 78.640
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


Mass: 31550.658 Da / Num. of mol.: 1 / Mutation: A129V
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PEG 3000, sodium phosphate/citrate, sodium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2004
RadiationMonochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→46.84 Å / Num. all: 42760 / Num. obs: 42732 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.062 / Net I/σ(I): 26
Reflection shellResolution: 1.65→1.71 Å / Mean I/σ(I) obs: 5.5 / Num. unique all: 4242 / Rsym value: 0.237 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1IUP

1iup


Resolution: 1.65→46.84 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1954847.71 / 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
Rfree0.191 2106 4.9 %RANDOM
Rwork0.173 ---
all0.174 42732 --
obs0.173 42703 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.0574 Å2 / ksol: 0.343085 e/Å3
Displacement parametersBiso mean: 14.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å20 Å20 Å2
2---1.63 Å20 Å2
3----1.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.65→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 11 372 2525
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_deg1.4
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_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it3.282
X-RAY DIFFRACTIONc_scangle_it4.62.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 354 5 %
Rwork0.203 6684 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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