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- PDB-1uiy: Crystal Structure of Enoyl-CoA Hydratase from Thermus Thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1uiy
TitleCrystal Structure of Enoyl-CoA Hydratase from Thermus Thermophilus HB8
ComponentsEnoyl-CoA Hydratase
KeywordsLYASE / beta-oxidation / crotonase / CoA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBagautdinov, B. / Kuramitsu, S. / Yokoyama, S. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8.
Authors: Padavattan, S. / Jos, S. / Gogoi, H. / Bagautdinov, B.
History
DepositionJul 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 19, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag / _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 / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA Hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6284
Polymers27,3561
Non-polymers2723
Water1,29772
1
A: Enoyl-CoA Hydratase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)165,76924
Polymers164,1366
Non-polymers1,63418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area36390 Å2
ΔGint-222 kcal/mol
Surface area50940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.233, 131.233, 110.608
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Enoyl-CoA Hydratase


Mass: 27355.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83702, enoyl-CoA hydratase
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.28 Å3/Da / Density % sol: 62.18 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.9
Details: Na Citrate 0.72M, Acetate 0.1M, pH 5.9, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 2002 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→40 Å / Num. all: 66615 / Num. obs: 15761 / % possible obs: 99.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.69 % / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.2
Reflection shellResolution: 2.85→2.98 Å / Redundancy: 5 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 5.7 / Num. unique all: 1684 / % possible all: 86.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DUB

2dub


Resolution: 2.85→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Refinement performed using anomalous f', f'' library file for Se at 0.98 Angstrom
RfactorNum. reflection% reflectionSelection details
Rfree0.267 778 -RANDOM
Rwork0.2035 ---
all-16595 --
obs-14983 95 %-
Displacement parametersBiso mean: 52.89 Å2
Baniso -1Baniso -2Baniso -3
1--7.06 Å20.75 Å20 Å2
2---7.06 Å20 Å2
3---14.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1907 0 18 72 1997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.85-2.980.309970.3080.031178186.2
2.98-3.140.298980.270.03197694.1
3.14-3.340.4910.2750.042184189.9
3.34-3.590.321910.2320.034197896.4
3.59-4.530.215950.1810.022206798.1
4.53-5.70.226970.1540.023203198.5

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