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- PDB-4jjt: The crystal structure of enoyl-CoA hydratase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 4jjt
TitleThe crystal structure of enoyl-CoA hydratase from Mycobacterium tuberculosis H37Rv
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / structural genomics / PSI-Biology / protein structure initiative / Midwest Center for Structural Genomics / MCSG / structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI
Function / homology
Function and homology information


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
ACETATE ION / Probable enoyl-CoA hydratase EchA16 (Enoyl hydrase) (Unsaturated acyl-CoA hydratase) (Crotonase)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.496 Å
AuthorsTan, K. / Holowicki, J. / Endres, M. / Kim, C.-Y. / Kim, H. / Hung, L.-W. / Terwilliger, T.C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: The crystal structure of enoyl-CoA hydratase from Mycobacterium tuberculosis H37Rv
Authors: Tan, K. / Holowicki, J. / Endres, M. / Kim, C.-Y. / Kim, H. / Hung, L.-W. / Terwilliger, T.C. / Joachimiak, A.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2Dec 6, 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

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase
C: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5557
Polymers81,2203
Non-polymers3354
Water3,387188
1
A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase
C: Enoyl-CoA hydratase
hetero molecules

A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase
C: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,11114
Polymers162,4406
Non-polymers6718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area20990 Å2
ΔGint-137 kcal/mol
Surface area47150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.318, 86.874, 80.957
Angle α, β, γ (deg.)90.00, 126.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

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Components

#1: Protein Enoyl-CoA hydratase /


Mass: 27073.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Mycobacterium tuberculosis, RVBD_2831 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: I6YEH6, enoyl-CoA hydratase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M sodium citrate, 20% (w/v) PEG4000, 5% (v/v) 2-propanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.5→40.5 Å / Num. all: 24439 / Num. obs: 24439 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1248 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 3P85

3p85


Resolution: 2.496→40.445 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1238 5.07 %random
Rwork0.1799 ---
obs0.1823 24425 95.66 %-
all-24425 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.496→40.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 22 188 5226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035107
X-RAY DIFFRACTIONf_angle_d0.6676952
X-RAY DIFFRACTIONf_dihedral_angle_d13.0361823
X-RAY DIFFRACTIONf_chiral_restr0.044842
X-RAY DIFFRACTIONf_plane_restr0.003904
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4957-2.59560.26981550.22882595X-RAY DIFFRACTION96
2.5956-2.71370.31151310.22412661X-RAY DIFFRACTION99
2.7137-2.85670.27151490.22262632X-RAY DIFFRACTION99
2.8567-3.03560.30651300.2162660X-RAY DIFFRACTION99
3.0356-3.26990.26431500.19712650X-RAY DIFFRACTION99
3.2699-3.59880.22041340.17542629X-RAY DIFFRACTION98
3.5988-4.11910.21421390.15482554X-RAY DIFFRACTION95
4.1191-5.18790.19771290.14722417X-RAY DIFFRACTION89
5.1879-40.44990.1761210.17682389X-RAY DIFFRACTION87
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)
14.7751.00611.62285.66761.25464.15450.2143-0.1505-0.41410.2573-0.0956-0.11440.30170.1118-0.10290.2480.0930.01630.25510.0420.2337-10.314-50.618317.444
23.80160.2774-0.71321.18840.00122.26080.02120.1173-0.1155-0.1236-0.0690.05210.133-0.09820.04310.24550.0354-0.00080.1767-0.01540.2067-18.7221-39.264415.5474
33.7073-1.69530.55156.2641-2.53193.48430.2990.2493-0.1227-0.3602-0.01710.3812-0.09-0.3571-0.30460.32420.04320.01730.48020.020.3633-51.497-23.926810.6687
49.6957-3.77293.03224.46071.84955.40040.0457-0.3082-0.86411.1671-0.08170.98220.4092-0.28460.06650.35160.04450.08250.38870.00570.3509-47.8445-34.408911.6869
52.11360.73630.37752.16970.39211.61650.00980.22550.1968-0.0671-0.0660.3188-0.256-0.20440.05560.29340.09960.00530.33470.01970.2704-39.3647-17.759612.5634
61.22340.27880.13672.5447-0.02251.92890.06660.1242-0.0248-0.1397-0.08940.1082-0.1102-0.1278-0.00140.15680.079-0.02130.29130.01150.206-33.7835-24.379713.585
78.2484-2.37190.11232.5240.10552.58050.29330.0840.9084-0.311-0.1055-0.4383-0.51690.1239-0.13480.5117-0.02790.12090.1859-0.03860.5194-5.01930.129616.7001
82.9586-0.46990.3413.8468-0.70383.6213-0.04940.01350.3722-0.10920.073-0.2528-0.32150.0833-0.02710.2412-0.01240.04860.23620.00580.2848-7.6063-11.770616.4854
92.6596-1.1402-0.38943.0399-0.31332.31650.23670.41630.2344-0.8184-0.0821-0.109-0.043-0.0869-0.08780.3377-0.01650.05060.29360.01650.2399-13.4994-14.67887.2042
104.4761-2.34120.46274.0981-1.49482.9386-0.0772-0.5910.12220.20280.1974-0.1518-0.10.19170.00650.253-0.07520.03440.2811-0.08760.1146-13.9906-16.337428.1759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 236 )
3X-RAY DIFFRACTION3chain 'B' and (resid 4 through 45 )
4X-RAY DIFFRACTION4chain 'B' and (resid 46 through 56 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 144 )
6X-RAY DIFFRACTION6chain 'B' and (resid 145 through 229 )
7X-RAY DIFFRACTION7chain 'C' and (resid 4 through 45 )
8X-RAY DIFFRACTION8chain 'C' and (resid 46 through 144 )
9X-RAY DIFFRACTION9chain 'C' and (resid 145 through 193 )
10X-RAY DIFFRACTION10chain 'C' and (resid 194 through 232 )

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