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- PDB-4lk5: Crystal structure of a enoyl-CoA hydratase from Mycobacterium avi... -

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Basic information

Entry
Database: PDB / ID: 4lk5
TitleCrystal structure of a enoyl-CoA hydratase from Mycobacterium avium subsp. paratuberculosis K-10
Componentsenoyl-CoA hydratase
KeywordsLYASE / PSI-BIOLOGY / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / New York Structural Genomics Research Consortium / NYSGRC / 028185 / alpha/beta / enoyl-CoA hydratase
Function / homology
Function and homology information


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 / 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 ...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 / 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
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Kumaran, D. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Al Obaidi, N. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of a enoyl-CoA hydratase from Mycobacterium avium subsp. paratuberculosis K-10
Authors: Kumaran, D. / Almo, S.C. / Swaminathan, S.
History
DepositionJul 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
C: enoyl-CoA hydratase


Theoretical massNumber of molelcules
Total (without water)91,8743
Polymers91,8743
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-55 kcal/mol
Surface area26380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.328, 78.328, 212.933
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein enoyl-CoA hydratase / EchA11


Mass: 30624.760 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Strain: K-10 / Gene: echA11, MAP_2639 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q73WM1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M Ammonium Acetate, 0.1M Sodium acetate, 30% PEG 4000 , pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2013 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 27170 / Num. obs: 27170 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / Num. unique all: 2640 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
Cootmodel building
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→49.04 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.019 / SU ML: 0.224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.558 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25777 1360 5 %RANDOM
Rwork0.19899 ---
all0.257 25753 --
obs0.20199 25753 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.28 Å20 Å2
2--0.28 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5271 0 0 71 5342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195356
X-RAY DIFFRACTIONr_bond_other_d0.0020.025338
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9937308
X-RAY DIFFRACTIONr_angle_other_deg0.862312243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38524.278187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.08515771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9041532
X-RAY DIFFRACTIONr_chiral_restr0.0850.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216077
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021081
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 99 -
Rwork0.238 1858 -
obs--99.39 %

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