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- PDB-1uk8: Crystal structure of a meta-cleavage product hydrolase (CumD) com... -

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Basic information

Entry
Database: PDB / ID: 1uk8
TitleCrystal structure of a meta-cleavage product hydrolase (CumD) complexed with n-valerate
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
PENTANOIC 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: 1.6 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)31,7113
Polymers31,5071
Non-polymers2042
Water6,936385
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)63,4226
Polymers63,0132
Non-polymers4094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)77.101, 116.001, 78.730
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-LEA / PENTANOIC ACID / VALERIC ACID


Mass: 102.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O2
#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: 2.48 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: PEG4000, AMMONIUM n-valerate, SODIUM n-valerate, 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: Mar 10, 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: 1.6→23.376 Å / Num. all: 46710 / Num. obs: 45682 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 13.5 Å2 / Rsym value: 0.067 / Net I/σ(I): 9.7
Reflection shellResolution: 1.6→1.69 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.271 / % possible all: 96.3

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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: 1.6→23.35 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1920006.16 / 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
Rfree0.19 2266 5 %RANDOM
Rwork0.178 ---
all0.179 45682 --
obs0.178 45658 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7339 Å2 / ksol: 0.330385 e/Å3
Displacement parametersBiso mean: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---0.89 Å20 Å2
3---0.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→23.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2139 0 14 385 2538
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_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.711.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it3.352
X-RAY DIFFRACTIONc_scangle_it4.752.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.254 382 5.1 %
Rwork0.212 7046 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NVA.PARAMNVA.TOP

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