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- PDB-3moy: Crystal structure of probable enoyl-CoA hydratase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3moy
TitleCrystal structure of probable enoyl-CoA hydratase from Mycobacterium smegmatis
ComponentsProbable enoyl-CoA hydratase
KeywordsLYASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / enoyl CoA / Actinobacteria
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity / fatty acid beta-oxidation
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
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 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 ...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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6148
Polymers28,0651
Non-polymers5507
Water4,179232
1
A: Probable enoyl-CoA hydratase
hetero molecules

A: Probable enoyl-CoA hydratase
hetero molecules

A: Probable enoyl-CoA hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,84324
Polymers84,1953
Non-polymers1,64921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area17360 Å2
ΔGint-162 kcal/mol
Surface area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.880, 84.880, 63.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-260-

SO4

21A-260-

SO4

31A-261-

TRS

41A-261-

TRS

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable enoyl-CoA hydratase


Mass: 28064.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084/ mc(2)155 / Gene: MSMEG_6777 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0R747, enoyl-CoA hydratase

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Non-polymers , 6 types, 239 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: JCSG+ screen condition D7, 40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4 with 20% ethylene glycol as cryo-protectant, 41.4 mg/mL protein in Tris buffer with 0.3 M NaCl and 10% glycerol, ...Details: JCSG+ screen condition D7, 40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4 with 20% ethylene glycol as cryo-protectant, 41.4 mg/mL protein in Tris buffer with 0.3 M NaCl and 10% glycerol, crystal tracking ID 215265d7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.5→35.29 Å / Num. obs: 41710 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.07 % / Biso Wilson estimate: 24.77 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 32.7
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 8.94 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 3.8 / Num. measured obs: 27548 / Num. unique obs: 3082 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.15 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å42.44 Å
Translation3 Å42.44 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: PDB ENTRY 3H81

3h81


Resolution: 1.5→35.29 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.16 / WRfactor Rwork: 0.151 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.91 / SU B: 2.215 / SU ML: 0.038 / SU R Cruickshank DPI: 0.064 / SU Rfree: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.168 2099 5 %RANDOM
Rwork0.153 ---
obs0.154 41665 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.4 Å2 / Biso mean: 20.39 Å2 / Biso min: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 34 232 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222047
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9892785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2815277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05722.96791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27915337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.721524
X-RAY DIFFRACTIONr_chiral_restr0.0860.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211554
X-RAY DIFFRACTIONr_mcbond_it0.7131.51313
X-RAY DIFFRACTIONr_mcangle_it1.26622101
X-RAY DIFFRACTIONr_scbond_it2.1713734
X-RAY DIFFRACTIONr_scangle_it3.5974.5674
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 146 -
Rwork0.211 2929 -
all-3075 -
obs--99.51 %
Refinement TLS params.Method: refined / Origin x: 42.1833 Å / Origin y: 42.888 Å / Origin z: 30.2572 Å
111213212223313233
T0.0391 Å20.0007 Å2-0.0307 Å2-0.0249 Å2-0.0032 Å2--0.0324 Å2
L0.4954 °20.02 °2-0.0041 °2-0.1541 °2-0.0339 °2--0.1566 °2
S-0.0453 Å °-0.0128 Å °0.0587 Å °-0.0104 Å °-0.016 Å °0.0002 Å °-0.0597 Å °-0.0097 Å °0.0613 Å °

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