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- PDB-4jfc: Crystal structure of a enoyl-CoA hydratase from Polaromonas sp. JS666 -

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Basic information

Entry
Database: PDB / ID: 4jfc
TitleCrystal structure of a enoyl-CoA hydratase from Polaromonas sp. JS666
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / PSI-BIOLOGY / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York Structural Genomics Research Consortium / NYSGRC / alpha/beta / Trimeric assembly / enoyl-CoA hydratase / Unsaturated fatty acyl-CoA
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity
Similarity search - Function
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
Biological speciesPolaromonas sp. JS666 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / 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 a enoyl-CoA hydratase from Polaromonas sp. JS666
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release

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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)30,0302
Polymers29,9381
Non-polymers921
Water91951
1
A: Enoyl-CoA hydratase
hetero molecules

A: Enoyl-CoA hydratase
hetero molecules

A: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0906
Polymers89,8133
Non-polymers2763
Water543
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
Buried area13640 Å2
ΔGint-91 kcal/mol
Surface area27250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.182, 111.182, 41.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Enoyl-CoA hydratase /


Mass: 29937.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Polaromonas sp. JS666 (bacteria) / Strain: JS666 / Gene: Bpro_2958 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q129C0, enoyl-CoA hydratase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.1M Tris, 0.2M MgCl2, 0.01M CsCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2013 / Details: Mirrors
RadiationMonochromator: Si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 13200 / Num. obs: 13200 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.7
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 1.5 / Num. unique all: 707 / % possible all: 64.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→48.19 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.743 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.251 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 651 4.9 %RANDOM
Rwork0.168 ---
obs0.17 12540 93.79 %-
all-12540 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.743 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.03 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 6 51 1949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191926
X-RAY DIFFRACTIONr_bond_other_d0.0020.021868
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9652609
X-RAY DIFFRACTIONr_angle_other_deg0.86334251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0865256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82924.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08615296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.9251516
X-RAY DIFFRACTIONr_chiral_restr0.1010.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02445
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.251→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 36 -
Rwork0.197 635 -
obs--64.64 %

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