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- PDB-1iq6: (R)-HYDRATASE FROM A. CAVIAE INVOLVED IN PHA BIOSYNTHESIS -

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Basic information

Entry
Database: PDB / ID: 1iq6
Title(R)-HYDRATASE FROM A. CAVIAE INVOLVED IN PHA BIOSYNTHESIS
Components(R)-SPECIFIC ENOYL-COA HYDRATASE
KeywordsLYASE / hydratase / (R)-hydratase / enoyl-CoA hydratase / polyhydroxyalkanoate / Aeromonas caviae / the hydratase 2 motif
Function / homology
Function and homology information


enoyl-CoA hydratase 2 / fatty acid synthase complex / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / fatty acid synthase activity / fatty acid biosynthetic process
Similarity search - Function
: / Fatty acid synthase / MaoC-like dehydratase domain / MaoC like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / (R)-specific enoyl-CoA hydratase
Similarity search - Component
Biological speciesAeromonas punctata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.5 Å
AuthorsHisano, T. / Tsuge, T. / Fukui, T. / Iwata, T. / Doi, Y.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of the (R)-specific enoyl-CoA hydratase from Aeromonas caviae involved in polyhydroxyalkanoate biosynthesis
Authors: Hisano, T. / Tsuge, T. / Fukui, T. / Iwata, T. / Miki, K. / Doi, Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: CRYSTALLIZATION AND PRELIMINARY X-RAY ANALYSIS OF (R)-SPECIFIC ENOYL-COA HYDRATASE FROM AEROMONAS CAVIAE INVOLVED IN POLYHYDROXYALKANOATE BIOSYNTHESIS
Authors: Hisano, T. / Fukui, T. / Iwata, T. / Doi, Y.
#2: Journal: J.BACTERIOL. / Year: 1998
Title: EXPRESSION AND CHARACTERIZATION OF (R)-SPECIFIC ENOYL-COA HYDRATASE INVOLVED IN POLYHYDROXYALKANOATE BIOSYNTHESIS BY AEROMONAS CAVIAE
Authors: Fukui, T. / SHIOMI, N. / Doi, Y.
#3: Journal: J.BACTERIOL. / Year: 1997
Title: CLONING AND ANALYSIS OF THE POLY(3-HYDROXYBUTYRATE-CO-3-HYDROXYHEXANOATE) BIOSYNTHESIS GENES OF AEROMONAS CAVIAE
Authors: Fukui, T. / Doi, Y.
History
DepositionJun 18, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (R)-SPECIFIC ENOYL-COA HYDRATASE
B: (R)-SPECIFIC ENOYL-COA HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2583
Polymers28,1982
Non-polymers601
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-17 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.03, 57.82, 46.97
Angle α, β, γ (deg.)90, 112.74, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein (R)-SPECIFIC ENOYL-COA HYDRATASE / (R)-HYDRATASE


Mass: 14099.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas punctata (bacteria) / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O32472, enoyl-CoA hydratase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Description: THE INITIAL STRUCTURE WAS DETERMINED AT 3.0 A RESOLUTION BY MIRAS WITH NATIVE DATA AND THREE SETS OF DERIVATIVE DATA, ALL OF WHICH WERE COLLECTED AT ROOM TEMPERATURE WITH A ROTATING ...Description: THE INITIAL STRUCTURE WAS DETERMINED AT 3.0 A RESOLUTION BY MIRAS WITH NATIVE DATA AND THREE SETS OF DERIVATIVE DATA, ALL OF WHICH WERE COLLECTED AT ROOM TEMPERATURE WITH A ROTATING ANODE X-RAY GENERATOR. THIS MODEL WAS USED TO PHASE THE 1.5 A DATA COLLECTED AT 100K WITH SYNCHROTRON RADIATION BY MOLECULAR REPLACEMENT, AND REFINED BY MOLECULAR DYNAMICS SIMULATION.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG4000, HEPES, ISOPROPANOL, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG40001reservoir
25 %2-propanol1reservoir
320 mMHEPES1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 52985 / % possible obs: 99.4 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.052
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 52985 / % possible obs: 99.4 % / Num. measured all: 198695 / Rmerge(I) obs: 0.052

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
PHASESphasing
CNS1refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MIRAS
Starting model: A STRUCTURE OF (R)-HYDRATASE FROM A.CAVIAE DETERMINED BY MIRAS AT 3.0 A RESOLUTION

Resolution: 1.5→19.15 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2183 5 %RANDOM
Rwork0.203 ---
obs0.203 43253 99.4 %-
all-43253 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.65 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.58 Å20 Å20.7 Å2
2--2.58 Å20 Å2
3---1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 0 351 2317
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_d24.7
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_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.612.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 373 5.1 %
Rwork0.246 6879 -
obs--100 %
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 19.15 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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