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- PDB-4jot: Crystal structure of enoyl-CoA hydrotase from Deinococcus radiodu... -

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Basic information

Entry
Database: PDB / ID: 4jot
TitleCrystal structure of enoyl-CoA hydrotase from Deinococcus radiodurans R1
ComponentsEnoyl-CoA hydratase, putative
KeywordsLYASE / NYSGRC / PSI-Biology / Structural Genomics / New York Structural Genomics Research Consortium / trimer / oxyanion hole
Function / homology
Function and homology information


Delta(3,5)-Delta(2,4)-dienoyl-CoA isomerase Ech1-like / 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 / Alpha Beta
Similarity search - Domain/homology
Enoyl-CoA hydratase, putative
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.94 Å
AuthorsEswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of enoyl-CoA hydrotase from Deinococcus radiodurans R1
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9042
Polymers29,8121
Non-polymers921
Water1,35175
1
A: Enoyl-CoA hydratase, putative
hetero molecules

A: Enoyl-CoA hydratase, putative
hetero molecules

A: Enoyl-CoA hydratase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7126
Polymers89,4353
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11320 Å2
ΔGint-78 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.892, 117.892, 117.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Enoyl-CoA hydratase, putative


Mass: 29811.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_0114 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9RY37
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000, TRIS.HCl, Sodium Acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2013 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 20369 / Num. obs: 20369 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.4
Reflection shellResolution: 1.94→2 Å / Redundancy: 21.6 % / Rmerge(I) obs: 0.39 / Num. unique all: 1680 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.94→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.944 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22007 1042 5.1 %RANDOM
Rwork0.19263 ---
obs0.194 19300 99.82 %-
all-20342 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.582 Å2
Refinement stepCycle: LAST / Resolution: 1.94→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 6 75 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221908
X-RAY DIFFRACTIONr_angle_refined_deg1.1141.9722593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4065254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73223.97373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0915303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7991513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211429
X-RAY DIFFRACTIONr_mcbond_it0.5811.51261
X-RAY DIFFRACTIONr_mcangle_it1.12721993
X-RAY DIFFRACTIONr_scbond_it2.0823647
X-RAY DIFFRACTIONr_scangle_it3.4094.5600
LS refinement shellResolution: 1.938→1.988 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 90 -
Rwork0.206 1374 -
obs-1464 99.73 %

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