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- PDB-3he2: Crystal structure of enoyl-CoA hydratase from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 3he2
TitleCrystal structure of enoyl-CoA hydratase from Mycobacterium tuberculosis
Componentsenoyl-CoA hydratase echA6
KeywordsLYASE / MYCOBACTERIUM TUBERCULOSIS / enoyl-CoA hydratase / Fatty acid metabolism / Lipid metabolism / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation / peptidoglycan-based cell wall / fatty acid metabolic process / plasma membrane
Similarity search - Function
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 / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Probable enoyl-CoA hydratase echA6 / Probable enoyl-CoA hydratase EchA6
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / Resolution: 2.3 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
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 6, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _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: enoyl-CoA hydratase echA6
B: enoyl-CoA hydratase echA6
C: enoyl-CoA hydratase echA6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4966
Polymers85,0453
Non-polymers4513
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-37 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.120, 76.470, 134.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: 5 / Auth seq-ID: 1 - 275 / Label seq-ID: 22

Dom-IDAuth asym-IDLabel asym-ID
1AA - G
2BB - H
3CC - I

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Components

#1: Protein enoyl-CoA hydratase echA6


Mass: 28348.330 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: 1719B / Gene: echA6, Rv0905, MT0928, MTCY31.33 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P64014, UniProt: P9WNP1*PLUS, enoyl-CoA hydratase
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: HAMPTON INDEX, H11: 30% PEG 2000 MME, 100MM KSCN, MYTUD.01381.A AT 32.5G/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→67.14 Å / Num. all: 32890 / Num. obs: 32742 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.85 % / Biso Wilson estimate: 34.83 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 67.14 / Net I/σ(I): 18.86
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 4.96 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2401 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: pdb entry 2qq3, modified with ccp4 program chainsaw

2qq3


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.412 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.36 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1661 5.1 %RANDOM
Rwork0.187 ---
all0.19 32695 --
obs0.19 32695 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.95 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å2-0 Å20 Å2
2---2.56 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5307 0 30 318 5655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225432
X-RAY DIFFRACTIONr_bond_other_d0.0010.023606
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9617369
X-RAY DIFFRACTIONr_angle_other_deg0.9338793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52823.874222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03115855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7291542
X-RAY DIFFRACTIONr_chiral_restr0.0830.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021053
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_it0.7271.53572
X-RAY DIFFRACTIONr_mcbond_other0.1671.51451
X-RAY DIFFRACTIONr_mcangle_it1.32925631
X-RAY DIFFRACTIONr_scbond_it2.26231860
X-RAY DIFFRACTIONr_scangle_it3.7094.51737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1398medium positional0.220.5
B1398medium positional0.290.5
C1398medium positional0.30.5
A1482loose positional0.555
B1482loose positional0.565
C1482loose positional0.585
A1398medium thermal1.772
B1398medium thermal2.372
C1398medium thermal2.412
A1482loose thermal1.9410
B1482loose thermal2.5810
C1482loose thermal2.5210
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 116 -
Rwork0.218 2283 -
obs--99.83 %

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