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- PDB-4r4u: Crystal structure of acyl-CoA thioesterase tesB from Yersinia pes... -

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Basic information

Entry
Database: PDB / ID: 4r4u
TitleCrystal structure of acyl-CoA thioesterase tesB from Yersinia pestis in complex with coenzyme A
ComponentsAcyl-CoA thioesterase II
KeywordsHYDROLASE / Double-HotDog / 4HBT-like / thioesterase / acyl-CoA thioesterase
Function / homology
Function and homology information


acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity
Similarity search - Function
Acyl-CoA thioesterase N-terminal domain / Acyl-CoA thioesterase / Acyl-CoA thioesterase, double hotdog domain / Acyl-CoA thioesterase, double hotdog domain / Porin / HotDog domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
COENZYME A / MALONIC ACID / Acyl-CoA thioesterase II
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSwarbrick, C.M.D. / Forwood, J.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and functional characterization of TesB from Yersinia pestis reveals a unique octameric arrangement of hotdog domains.
Authors: Swarbrick, C.M. / Perugini, M.A. / Cowieson, N. / Forwood, J.K.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Non-polymer description
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Sep 20, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: Acyl-CoA thioesterase II
D: Acyl-CoA thioesterase II
C: Acyl-CoA thioesterase II
B: Acyl-CoA thioesterase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7819
Polymers131,0964
Non-polymers1,6855
Water7,458414
1
A: Acyl-CoA thioesterase II
B: Acyl-CoA thioesterase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3394
Polymers65,5482
Non-polymers7912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Acyl-CoA thioesterase II
C: Acyl-CoA thioesterase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4435
Polymers65,5482
Non-polymers8953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.976, 171.369, 73.656
Angle α, β, γ (deg.)90.00, 109.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acyl-CoA thioesterase II


Mass: 32773.996 Da / Num. of mol.: 4 / Fragment: TesB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: KIM 10 / Gene: tesB, y1043, YPO3141, YP_0790 / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 pLysS / References: UniProt: Q8D151
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG 3350, 200 mM sodium malonate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 9, 2014
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→45.91 Å / Num. obs: 60243 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4QFW

4qfw


Resolution: 2.2→85.68 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.667 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26592 2995 5 %RANDOM
Rwork0.20137 ---
obs0.20454 57177 99.93 %-
all-60167 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.2→85.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8607 0 105 414 9126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198950
X-RAY DIFFRACTIONr_bond_other_d0.0020.028279
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.96212116
X-RAY DIFFRACTIONr_angle_other_deg0.791319026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65351067
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6823.589457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7531571
X-RAY DIFFRACTIONr_chiral_restr0.080.21258
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110197
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022200
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_it2.8143.514301
X-RAY DIFFRACTIONr_mcbond_other2.8143.5094300
X-RAY DIFFRACTIONr_mcangle_it4.1375.2455357
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2193.9044649
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 214 -
Rwork0.295 4208 -
obs--99.91 %

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