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- PDB-3ome: Crystal structure of a probable ENOYL-COA Hydratase from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 3ome
TitleCrystal structure of a probable ENOYL-COA Hydratase from Mycobacterium Smegmatis
ComponentsEnoyl-CoA hydratase
KeywordsLYASE / SSGCID / ENOYL-COA HYDRATASE / HYDRATASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity / metal ion binding
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
Probable enoyl-CoA hydratase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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_ncs_dom_lim.end_label_seq_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
B: Enoyl-CoA hydratase
C: Enoyl-CoA hydratase
D: Enoyl-CoA hydratase
E: Enoyl-CoA hydratase
F: Enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,86712
Polymers186,4756
Non-polymers3926
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23540 Å2
ΔGint-366 kcal/mol
Surface area44700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.220, 86.650, 140.050
Angle α, β, γ (deg.)90.00, 97.93, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA1 - 6423 - 86
21VALVALBB1 - 6423 - 86
31VALVALCC1 - 6423 - 86
41VALVALDD1 - 6423 - 86
51VALVALEE1 - 6423 - 86
61VALVALFF1 - 6423 - 86
12LYSLYSAA73 - 24995 - 271
22LYSLYSBB73 - 24995 - 271
32LYSLYSCC73 - 24995 - 271
42LYSLYSDD73 - 24995 - 271
52LYSLYSEE73 - 24995 - 271
62LYSLYSFF73 - 24995 - 271
DetailsBIOMOLECULE: NULL SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. REMARK: BIOLOGICAL UNIT IS A HEXAMER, THE SAME AS ASU

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Components

#1: Protein
Enoyl-CoA hydratase


Mass: 31079.162 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_4846 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0R1R4, enoyl-CoA hydratase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.53 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: EBS JCSG+ SCEEN E11: 160MM CAOAC2, 80MM CACODYLATE PH 6.5, 14.4% PEG 8000, 20% GLYCEROL, MYSMA.00358.E.A1 PS00544 AT 30MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 108008 / Num. obs: 107914 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 35.58 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.89
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7953 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3h8l

3h8l


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.816 / SU ML: 0.082 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.174 5373 5 %RANDOM
Rwork0.145 ---
all0.147 108008 --
obs0.147 107778 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-0.47 Å2
2--1.23 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11189 0 6 666 11861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02111470
X-RAY DIFFRACTIONr_bond_other_d0.0010.027560
X-RAY DIFFRACTIONr_angle_refined_deg1.341.94515623
X-RAY DIFFRACTIONr_angle_other_deg0.93318354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43251469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10823.54531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.559151781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.151598
X-RAY DIFFRACTIONr_chiral_restr0.0870.21777
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022367
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_it0.7261.57305
X-RAY DIFFRACTIONr_mcbond_other0.1961.52974
X-RAY DIFFRACTIONr_mcangle_it1.345211645
X-RAY DIFFRACTIONr_scbond_it2.29634165
X-RAY DIFFRACTIONr_scangle_it3.7384.53971
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 / Number: 2965 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.245
Bloose positional0.255
Cloose positional0.275
Dloose positional0.245
Eloose positional0.255
Floose positional0.25
Aloose thermal1.3710
Bloose thermal1.5610
Cloose thermal2.110
Dloose thermal1.3410
Eloose thermal1.7210
Floose thermal1.8710
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 373 -
Rwork0.214 7538 -
obs-7940 99.68 %
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)
10.83260.16050.1160.6388-0.0911.85950.01210.23920.0476-0.1171-0.0687-0.1032-0.17080.28990.05670.22410.01190.01770.2920.05350.042238.36562.40418.205
21.10110.07160.07630.6142-0.29792.0342-0.01030.13990.036-0.07970.04590.1617-0.0169-0.4682-0.03560.18320.0441-0.06370.3450.0010.06565.32857.63722.303
30.99220.01370.44560.76440.2562.22330.10.1683-0.2167-0.0276-0.0304-0.19850.47350.6326-0.06950.290.1919-0.01270.3441-0.00520.140346.76535.70933.837
40.9316-0.14170.20550.5513-0.36161.85190.0346-0.1-0.16670.0726-0.00410.06310.3188-0.2032-0.03050.3072-0.0395-0.01750.17270.04070.069120.62836.27254.783
50.98860.03080.08790.57960.14081.52770.0154-0.11260.1210.0575-0.06440.0108-0.2937-0.06030.0490.2630.02-0.0240.1631-0.02540.035224.26667.56648.632
60.91890.0508-0.28450.7546-0.07222.18090.03720.2427-0.3186-0.153-0.03090.09160.6486-0.3152-0.00640.4694-0.0565-0.07170.2543-0.11160.155616.03127.54722.115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3D-10 - 9999
4X-RAY DIFFRACTION4E-10 - 9999
5X-RAY DIFFRACTION5C-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999

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