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- PDB-5kjp: Crystal structure of enoyl-CoA hydratase from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 5kjp
TitleCrystal structure of enoyl-CoA hydratase from Mycobacterium tuberculosis H37Rv
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / fatty acids metabolism / Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


enoyl-CoA hydratase activity / fatty acid beta-oxidation
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
Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsNocek, B. / Hatzos-Skintges, C. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of enoyl-CoA hydratase from Mycobacterium tuberculosis H37Rv
Authors: Nocek, B. / Hatzos-Skintges, C. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)27,8621
Polymers27,8621
Non-polymers00
Water3,873215
1
A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)83,5863
Polymers83,5863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8930 Å2
ΔGint-77 kcal/mol
Surface area30220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.476, 121.476, 121.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

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Components

#1: Protein Enoyl-CoA hydratase / Probable enoyl-CoA hydratase EchA1 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)


Mass: 27861.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: echA1, Rv0222, LH57_01220 / Production host: Escherichia coli (E. coli) / References: UniProt: P96404, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Ammonium Sulfate 0.1 M Bis-Tris:HCl pH 6.5 25% (w/v) PEG 3350
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→28.632 Å / Num. obs: 40251 / % possible obs: 97.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 9

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→28.632 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.86 / Phase error: 17.84
RfactorNum. reflection% reflection
Rfree0.1838 2025 5.03 %
Rwork0.1534 --
obs0.1549 40251 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 0 216 2064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051908
X-RAY DIFFRACTIONf_angle_d0.8992592
X-RAY DIFFRACTIONf_dihedral_angle_d11.982714
X-RAY DIFFRACTIONf_chiral_restr0.034302
X-RAY DIFFRACTIONf_plane_restr0.004346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.84510.2237490.2466913X-RAY DIFFRACTION25
1.8451-1.8950.2874720.2021403X-RAY DIFFRACTION38
1.895-1.95070.2102940.18131854X-RAY DIFFRACTION50
1.9507-2.01370.19381370.16642051X-RAY DIFFRACTION58
2.0137-2.08560.19251190.15722426X-RAY DIFFRACTION66
2.0856-2.16910.15641340.15472719X-RAY DIFFRACTION75
2.1691-2.26780.17281790.14963000X-RAY DIFFRACTION83
2.2678-2.38730.15091880.15173147X-RAY DIFFRACTION87
2.3873-2.53680.22931720.15773357X-RAY DIFFRACTION92
2.5368-2.73250.17741660.15723399X-RAY DIFFRACTION94
2.7325-3.00720.1951640.1613594X-RAY DIFFRACTION96
3.0072-3.44170.1851840.1523530X-RAY DIFFRACTION98
3.4417-4.33380.16371930.13553542X-RAY DIFFRACTION98
4.3338-28.63580.19491740.1533291X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.50080.0503-0.0512.4504-0.78041.49790.08330.1840.0094-0.5604-0.182-0.26770.09380.14560.09310.24420.07430.05820.19760.03420.133844.41224.15782.3697
21.7503-0.8844-0.37341.1823-0.59440.8730.11210.07310.0512-0.1195-0.08620.036-0.0014-0.0138-0.03160.12060.01810.00210.12930.01220.097433.773729.509913.1327
31.22340.2928-0.49851.7488-0.25981.371-0.09960.1351-0.129-0.0991-0.02230.09030.2744-0.07390.11020.16450.0260.01530.1327-0.00690.129733.45948.225818.8783
43.2290.10011.11332.7337-0.93315.82490.02830.1113-0.01020.3557-0.0637-0.6369-0.1170.2240.02210.34110.03160.04250.14360.0240.299947.8323-2.013525.1027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 189 )
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 241 )
4X-RAY DIFFRACTION4chain 'A' and (resid 242 through 262 )

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