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- PDB-3h81: Crystal structure of enoyl-CoA hydratase from Mycobacterium tuber... -

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Basic information

Entry
Database: PDB / ID: 3h81
TitleCrystal structure of enoyl-CoA hydratase from Mycobacterium tuberculosis
Componentsenoyl-CoA hydratase echA8
KeywordsLYASE / NIAID / deCODE / infectious disease / MPCS / 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
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 echA8 / Probable enoyl-CoA hydratase EchA8
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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_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.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_conn.ptnr2_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 echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,25710
Polymers88,7693
Non-polymers4897
Water12,629701
1
A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules

A: enoyl-CoA hydratase echA8
B: enoyl-CoA hydratase echA8
C: enoyl-CoA hydratase echA8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,51520
Polymers177,5386
Non-polymers97714
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area35140 Å2
ΔGint-304 kcal/mol
Surface area47130 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-138 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.853, 130.947, 102.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-287-

HOH

21B-302-

HOH

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Components

#1: Protein enoyl-CoA hydratase echA8


Mass: 29589.594 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: echA8, Rv1070c, MT1100, MTV017.23c / Production host: Escherichia coli (E. coli)
References: UniProt: P64016, UniProt: P9WNN9*PLUS, enoyl-CoA hydratase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Wizard Full condition F6: 0.1 M Tris, 20% PEG 3000, 0.2 M CaCl2, crystal ID 208527F6, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDate: Apr 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→93.6 Å / Num. obs: 80982 / % possible obs: 97.5 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.083 / Χ2: 1.108 / Net I/σ(I): 21.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.69 / Num. unique all: 6722 / Χ2: 0.821 / % possible all: 81.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1DUB

1dub


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.877 / SU B: 2.226 / SU ML: 0.068 / SU R Cruickshank DPI: 0.115 / SU Rfree: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 4073 5 %RANDOM
Rwork0.174 ---
obs0.175 80847 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.71 Å2 / Biso mean: 22.9 Å2 / Biso min: 8.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5637 0 27 701 6365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225869
X-RAY DIFFRACTIONr_bond_other_d0.0010.023855
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.9657971
X-RAY DIFFRACTIONr_angle_other_deg0.85839419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0285800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.49423.863233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.55315957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1981546
X-RAY DIFFRACTIONr_chiral_restr0.0620.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026772
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021191
X-RAY DIFFRACTIONr_mcbond_it0.4741.53906
X-RAY DIFFRACTIONr_mcbond_other0.091.51603
X-RAY DIFFRACTIONr_mcangle_it0.90326218
X-RAY DIFFRACTIONr_scbond_it1.49831963
X-RAY DIFFRACTIONr_scangle_it2.5944.51753
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 259 -
Rwork0.275 4501 -
all-4760 -
obs--78.95 %

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