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- PDB-3sll: Crystal structure of a probable enoyl-CoA hydratase/isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 3sll
TitleCrystal structure of a probable enoyl-CoA hydratase/isomerase from Mycobacterium abscessus
ComponentsProbable enoyl-CoA hydratase/isomerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium / enoyl-coA / fatty acid biosynthesis
Function / homology
Function and homology information


enoyl-CoA hydratase activity / isomerase 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
Probable enoyl-CoA hydratase/isomerase
Similarity search - Component
Biological speciesMycobacterium abscessus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJun 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 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_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_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

Downloads & links

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Assembly

Deposited unit
A: Probable enoyl-CoA hydratase/isomerase
B: Probable enoyl-CoA hydratase/isomerase
C: Probable enoyl-CoA hydratase/isomerase
D: Probable enoyl-CoA hydratase/isomerase
E: Probable enoyl-CoA hydratase/isomerase
F: Probable enoyl-CoA hydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,56315
Polymers188,9046
Non-polymers6599
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36800 Å2
ΔGint-207 kcal/mol
Surface area45840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.090, 131.650, 148.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Probable enoyl-CoA hydratase/isomerase


Mass: 31484.080 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium abscessus (bacteria) / Strain: ATCC 19977 / DSM 44196 / Gene: MAB_2737c / Production host: Escherichia coli (E. coli) / References: UniProt: B1MC45
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MyabA.00305.a.A1 at 34.6 mg/mL against JCSG+ screen condition B12, 0.2 M potassium citrate, 20% PEG 3350 with 25% ethylene glycol as cryo-protection reagent, crystal tracking ID 219708b12, ...Details: MyabA.00305.a.A1 at 34.6 mg/mL against JCSG+ screen condition B12, 0.2 M potassium citrate, 20% PEG 3350 with 25% ethylene glycol as cryo-protection reagent, crystal tracking ID 219708b12, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 66204 / Num. obs: 65136 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 29.276 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 13.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.35-2.416.80.4694.3326554840483599.9
2.41-2.480.4084.9932415469799.9
2.48-2.550.3685.66320704579100
2.55-2.630.3336.28316544441100
2.63-2.710.2827.5311594328100
2.71-2.810.2747.68305614205100
2.81-2.910.2279.24295064042100
2.91-3.030.20610.03284273884100
3.03-3.170.16811.88274103746100
3.17-3.320.13814.02262923608100
3.32-3.50.12515.9924415340299.8
3.5-3.720.09518.4714812253078.2
3.72-3.970.1118.3916865275189.9
3.97-4.290.07224.3320089283299.6
4.29-4.70.06526.46186012642100
4.7-5.250.06525.5816768238899.9
5.25-6.070.07221.85147082129100
6.07-7.430.05824.35130931825100
7.43-10.510.03634.58100841435100
10.510.02937.01546083798.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.78 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.12 Å
Translation2.5 Å48.12 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h81

3h81


Resolution: 2.35→50 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.855 / WRfactor Rfree: 0.2272 / WRfactor Rwork: 0.1804 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8423 / SU B: 14.727 / SU ML: 0.165 / SU R Cruickshank DPI: 0.4717 / SU Rfree: 0.2756 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2578 3299 5.1 %RANDOM
Rwork0.2026 ---
obs0.2054 64902 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.28 Å2 / Biso mean: 20.4687 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.63 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11634 0 39 466 12139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211844
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.97916040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04851558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.97122.79491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87151933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5715124
X-RAY DIFFRACTIONr_chiral_restr0.0920.21879
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218914
X-RAY DIFFRACTIONr_mcbond_it0.5921.57762
X-RAY DIFFRACTIONr_mcangle_it1.086212326
X-RAY DIFFRACTIONr_scbond_it1.96234082
X-RAY DIFFRACTIONr_scangle_it3.0924.53712
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 235 -
Rwork0.177 4584 -
all-4819 -
obs--99.69 %
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)
10.2605-0.00820.06410.33540.00250.3157-0.0076-0.0501-0.01460.02340.0002-0.02-0.00470.04040.00750.03170.0067-0.00820.04390.00180.030134.9997-1.902139.7439
20.68930.12230.16030.28280.07340.2523-0.0184-0.0140.07090.0093-0.01410.0163-0.1035-0.03820.03260.0680.0221-0.01950.0084-0.0060.030120.073123.996228.7713
30.3002-0.10220.07490.28840.03620.4433-0.0043-0.0494-0.03850.02190.01750.03040.0149-0.1207-0.01320.00270.00240.00240.07180.01980.02813.8737-2.836932.6311
40.39020.1435-0.08140.326-0.22350.3027-0.02430.0474-0.0472-0.03850.005-0.04750.02040.06040.01920.02530.00460.01190.0368-0.01430.042643.428-6.717910.8719
50.3998-0.0457-0.04750.3248-0.06790.1839-0.00990.0288-0.0501-0.07590.02470.03430.0554-0.0563-0.01480.0419-0.0104-0.02050.0382-0.01850.033813.2845-14.42515.5096
60.5285-0.0054-0.04810.01090.02720.4478-0.0470.14410.0027-0.01980.009-0.0022-0.1076-0.03960.0380.0689-0.0122-0.00370.06190.00150.010623.816615.1018-0.5642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 269
4X-RAY DIFFRACTION2B1 - 269
7X-RAY DIFFRACTION3C2 - 269
10X-RAY DIFFRACTION4D3 - 269
13X-RAY DIFFRACTION5E2 - 269
16X-RAY DIFFRACTION6F2 - 269

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