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- PDB-3njd: Crystal structure of enoyl-coa hydratase from mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 3njd
TitleCrystal structure of enoyl-coa hydratase from mycobacterium smegmatis
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / SSGCID / ENOYL-COA HYDRATASE / MYCOBACERIUM SMEGMATIS / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


lipid metabolic process / lyase activity
Similarity search - Function
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
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Apr 15, 2015Group: Database references
Revision 1.4Sep 6, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)72,0112
Polymers72,0112
Non-polymers00
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-13 kcal/mol
Surface area25110 Å2
MethodPISA
2
A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase
B: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)216,0346
Polymers216,0346
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27420 Å2
ΔGint-177 kcal/mol
Surface area54640 Å2
MethodPISA
3
A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase

A: Enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)108,0173
Polymers108,0173
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8200 Å2
ΔGint-48 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.010, 171.010, 171.010
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
11B-642-

HOH

21B-667-

HOH

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Components

#1: Protein Enoyl-CoA hydratase /


Mass: 36005.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / MC(2)155 / Gene: MSMEG_1388 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QS86, enoyl-CoA hydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 3.04 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MD PACT SCEEN H12: 200MM NAMALONATE, 100M BISTRISPROPANE, 20% PEG 3350; protein at 27MG/ML, CRYO: 15% EDO, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 83314 / Num. obs: 83011 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.1
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5999 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3NJB

3njb


Resolution: 1.75→42.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.165 / SU ML: 0.045 / Isotropic thermal model: TLS, isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.165 4087 4.9 %RANDOM
Rwork0.144 ---
all0.145 82903 --
obs0.145 82903 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4367 0 0 641 5008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214541
X-RAY DIFFRACTIONr_bond_other_d0.0010.022979
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.9466207
X-RAY DIFFRACTIONr_angle_other_deg0.99637254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3255606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61323.544206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2715686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.731538
X-RAY DIFFRACTIONr_chiral_restr0.0990.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02929
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_it0.8751.52935
X-RAY DIFFRACTIONr_mcbond_other0.2881.51194
X-RAY DIFFRACTIONr_mcangle_it1.50224702
X-RAY DIFFRACTIONr_scbond_it2.40231606
X-RAY DIFFRACTIONr_scangle_it3.7114.51491
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 299 -
Rwork0.259 5682 -
obs--98.16 %
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)
10.5017-0.1077-0.13380.30590.04560.2946-0.00790.0080.0894-0.02180.0069-0.0233-0.09320.01950.0010.047-0.0068-0.00380.00240.00470.047940.23463.30634.301
20.5021-0.1945-0.14660.26460.05180.26240.01490.1010.003-0.0919-0.0150.0234-0.008-0.0290.00010.0520.0008-0.01010.05840.00270.003435.04339.21110.882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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