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- PDB-3sps: Crystal Structure of Apo-Hexameric Acyl-CoA Thioesterase -

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Basic information

Entry
Database: PDB / ID: 3sps
TitleCrystal Structure of Apo-Hexameric Acyl-CoA Thioesterase
ComponentsAcyl-CoA hydrolase
KeywordsHYDROLASE / Hotdog / Thioesterase
Function / homology
Function and homology information


thiolester hydrolase activity
Similarity search - Function
Hotdog acyl-CoA thioesterase (ACOT)-type domain / Hotdog acyl-CoA thioesterase (ACOT)-type domain profile. / Cytosolic acyl coenzyme A thioester hydrolase / Thioesterase domain / Thioesterase superfamily / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsForwood, J.K. / Marfori, M. / Kobe, B.
CitationJournal: To be Published
Title: Ligand-Induced Conformational Changes within a Hexameric Acyl-CoA Thioesterase
Authors: Forwood, J.K. / Marfori, M. / Kobe, B.
History
DepositionJul 3, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA hydrolase
B: Acyl-CoA hydrolase
C: Acyl-CoA hydrolase
D: Acyl-CoA hydrolase
E: Acyl-CoA hydrolase
F: Acyl-CoA hydrolase


Theoretical massNumber of molelcules
Total (without water)112,8806
Polymers112,8806
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15880 Å2
ΔGint-95 kcal/mol
Surface area37080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.179, 78.544, 187.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Acyl-CoA hydrolase /


Mass: 18813.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125 / Gene: BH0798 / Plasmid: pBAD/HIS / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KEQ1, Hydrolases; Acting on ester bonds; Thioester hydrolases

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 22 % PEG 3350, 0.13-0.17 M sodium formate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. obs: 23985

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VPM

1vpm


Resolution: 2.9→24.57 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 46.321 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28671 1210 5.1 %RANDOM
Rwork0.23125 ---
all0.28671 22694 --
obs0.23405 22694 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.587 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 0 0 0 7215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227335
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.031.9739951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0755927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07723.592309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.422151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7631563
X-RAY DIFFRACTIONr_chiral_restr0.0620.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025415
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.23072
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2890.25031
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2611.54787
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.46627599
X-RAY DIFFRACTIONr_scbond_it0.50832771
X-RAY DIFFRACTIONr_scangle_it0.9034.52352
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 79 -
Rwork0.294 1638 -
obs--99.42 %
Refinement TLS params.Method: refined / Origin x: -10.5935 Å / Origin y: 0.0394 Å / Origin z: 70.4056 Å
111213212223313233
T-0.0964 Å2-0.0986 Å2-0.0019 Å2--0.2446 Å20.0048 Å2---0.1517 Å2
L1.9495 °2-0.1328 °2-0.1163 °2-1.0026 °20.0534 °2--1.1213 °2
S0.1658 Å °-0.3783 Å °0.0226 Å °0.2423 Å °-0.1301 Å °0.0411 Å °0.0326 Å °-0.1172 Å °-0.0357 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 157
2X-RAY DIFFRACTION1B2 - 157
3X-RAY DIFFRACTION1C2 - 156
4X-RAY DIFFRACTION1D2 - 156
5X-RAY DIFFRACTION1E2 - 157
6X-RAY DIFFRACTION1F2 - 156

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