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- PDB-3d6l: Crystal structure of Cj0915, a hexameric hotdog fold thioesterase... -

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Basic information

Entry
Database: PDB / ID: 3d6l
TitleCrystal structure of Cj0915, a hexameric hotdog fold thioesterase of Campylobacter jejuni
ComponentsPutative hydrolase
KeywordsHYDROLASE / hot dog fold / thioesterase / acyl-CoA / Campylobacter jejuni
Function / homology
Function and homology information


long-chain fatty acyl-CoA hydrolase activity / acyl-CoA metabolic process / fatty acid catabolic process / cytosol
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Cytosolic acyl coenzyme A thioester hydrolase / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsYokoyama, T. / Yeo, H.J.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Structure and function of a Campylobacter jejuni thioesterase Cj0915, a hexameric hot dog fold enzyme.
Authors: Yokoyama, T. / Choi, K.J. / Bosch, A.M. / Yeo, H.J.
History
DepositionMay 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8433
Polymers14,7721
Non-polymers712
Water36020
1
A: Putative hydrolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)89,05718
Polymers88,6326
Non-polymers42512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
crystal symmetry operation18_445-x-3/4,z-1/4,y+1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area13930 Å2
ΔGint-229 kcal/mol
Surface area31610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.018, 103.018, 103.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Putative hydrolase


Mass: 14771.989 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: Cj0915 / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q0P9Y4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.75M NaCl, 0.1M Sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97915 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 6240 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 5.6
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.339 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YLI

1yli


Resolution: 2.59→24.28 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.076 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.408 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25971 286 4.6 %RANDOM
Rwork0.20651 ---
obs0.20893 5920 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.323 Å2
Refinement stepCycle: LAST / Resolution: 2.59→24.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 2 20 1024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221016
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9671377
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2535132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.05524.73738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.59115181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.418156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02738
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2409
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.2702
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5751.5677
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05821079
X-RAY DIFFRACTIONr_scbond_it1.1693374
X-RAY DIFFRACTIONr_scangle_it2.1344.5298
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 21 -
Rwork0.239 416 -
obs--100 %

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