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- PDB-4k2n: Crystal structure of an enoyl-CoA hydratase/ carnithine racemase ... -

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Basic information

Entry
Database: PDB / ID: 4k2n
TitleCrystal structure of an enoyl-CoA hydratase/ carnithine racemase from Magnetospirillum magneticum
ComponentsEnoyl-CoA hydratase/carnithine racemase
KeywordsISOMERASE / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / crotonase-like / oxyanion hole
Function / homology
Function and homology information


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 / 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
Enoyl-CoA hydratase/carnithine racemase
Similarity search - Component
Biological speciesMagnetospirillum magneticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsEswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / Gizzi, A. / Hillerich, B. / Kar, A. / Lafleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, F. / 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 an enoyl-CoA hydratase/ carnithine racemase from Magnetospirillum magneticum
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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/carnithine racemase


Theoretical massNumber of molelcules
Total (without water)30,9751
Polymers30,9751
Non-polymers00
Water95553
1
A: Enoyl-CoA hydratase/carnithine racemase

A: Enoyl-CoA hydratase/carnithine racemase

A: Enoyl-CoA hydratase/carnithine racemase


Theoretical massNumber of molelcules
Total (without water)92,9263
Polymers92,9263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area10580 Å2
ΔGint-69 kcal/mol
Surface area30820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.310, 120.310, 120.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Enoyl-CoA hydratase/carnithine racemase


Mass: 30975.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum (bacteria) / Strain: AMB-1 / Gene: amb1315 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2W7Q6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium Chloride, HEPES, PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2013 / Details: MIRRORS
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 19654 / Num. obs: 19654 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 33.3 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 33.6 % / Rmerge(I) obs: 0.667 / Num. unique all: 1927 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→42.57 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.969 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2119 1005 5.1 %RANDOM
Rwork0.19471 ---
all0.2278 19654 --
obs0.1956 18637 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.562 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 53 2083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192063
X-RAY DIFFRACTIONr_bond_other_d0.0010.022027
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9812795
X-RAY DIFFRACTIONr_angle_other_deg0.77434643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57523.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87615325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5391521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 65 -
Rwork0.261 1368 -
obs-1433 100 %

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