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- PDB-7cz3: Crystal strcuture of Acyl-CoA thioesterase from Bacillus cereus A... -

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Basic information

Entry
Database: PDB / ID: 7cz3
TitleCrystal strcuture of Acyl-CoA thioesterase from Bacillus cereus ATCC 14579
ComponentsAcyl-CoA hydrolase
KeywordsHYDROLASE / hotdog domain
Function / homology
Function and homology information


acyl-CoA hydrolase / long-chain fatty acyl-CoA binding / acyl-CoA metabolic process / fatty acyl-CoA hydrolase activity / fatty acid metabolic process / DNA binding / cytosol
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 domain superfamily
Similarity search - Domain/homology
COENZYME A / Acyl-CoA hydrolase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsPark, J. / Kim, K.-J.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural basis for nucleotide-independent regulation of acyl-CoA thioesterase from Bacillus cereus ATCC 14579.
Authors: Park, J. / Kim, Y.J. / Lee, D. / Kim, K.J.
History
DepositionSep 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,66912
Polymers121,0646
Non-polymers4,6056
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26300 Å2
ΔGint-100 kcal/mol
Surface area40180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.685, 78.685, 215.634
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Acyl-CoA hydrolase


Mass: 20177.252 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / Gene: BC_5426 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q814K4, acyl-CoA hydrolase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.36 Å3/Da / Density % sol: 63.41 % / Mosaicity: 0.858 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Sodium phosphate monobasic monohydrate, Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 23, 2020
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 30899 / % possible obs: 92.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.046 / Rrim(I) all: 0.095 / Χ2: 3.583 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.9540.36715410.940.1890.4152.18493.1
2.95-33.90.315760.9810.1550.3392.13694.3
3-3.063.90.25715850.9610.1330.292.40793
3.06-3.123.90.22115600.9690.1150.252.49594.3
3.12-3.193.90.19315390.9760.10.2182.65792.3
3.19-3.273.80.15715890.9860.0820.1782.99293.6
3.27-3.353.80.14115170.9870.0740.1593.18293.8
3.35-3.443.70.11516000.990.0610.133.50892.3
3.44-3.543.80.10615430.9910.0570.1213.63393.8
3.54-3.653.70.115400.9910.0530.1143.95393.2
3.65-3.783.70.09815720.990.0530.1114.16292.7
3.78-3.943.70.0915500.9910.0490.1034.17792.8
3.94-4.113.70.08115740.9930.0450.0934.45994.3
4.11-4.333.60.07415330.9940.0410.0854.58992.9
4.33-4.63.50.06615660.9920.0370.0764.71493.3
4.6-4.963.50.06315580.9930.0360.0734.53892.8
4.96-5.463.60.06415740.9930.0360.0734.52294.4
5.46-6.243.70.06415950.9920.0360.0744.20795.1
6.24-7.863.60.05815610.9930.0330.0674.03293.7
7.86-5030.05212260.9910.0350.0634.03872.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y7U

1y7u


Resolution: 2.9→30.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.889 / SU B: 17.784 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2764 1531 5 %RANDOM
Rwork0.1874 ---
obs0.1918 29334 92.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.38 Å2 / Biso mean: 74.41 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å21.06 Å2-0 Å2
2--2.13 Å2-0 Å2
3----6.89 Å2
Refinement stepCycle: final / Resolution: 2.9→30.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7739 0 288 20 8047
Biso mean--81.41 40.5 -
Num. residues----986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138150
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177721
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.65411021
X-RAY DIFFRACTIONr_angle_other_deg1.2241.5817932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4095980
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62721.36397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.738151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7961554
X-RAY DIFFRACTIONr_chiral_restr0.0690.21112
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028816
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021644
LS refinement shellResolution: 2.891→2.966 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 103 -
Rwork0.308 2199 -
all-2302 -
obs--92.19 %

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