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- PDB-3rd7: Crystal structure of acyl-coa thioesterase from mycobacterium avium -

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Basic information

Entry
Database: PDB / ID: 3rd7
TitleCrystal structure of acyl-coa thioesterase from mycobacterium avium
ComponentsAcyl-CoA thioesterase
KeywordsHYDROLASE / ACYL-COA THIOESTERASE / MYCOBACTERIUM AVIUM / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
Acyl-CoA thioesterase / Acyl-CoA thioesterase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Acyl-CoA thioesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4324
Polymers63,3622
Non-polymers712
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-44 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.750, 62.800, 82.220
Angle α, β, γ (deg.)90.00, 99.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acyl-CoA thioesterase


Mass: 31680.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_2540 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QFP4, UniProt: A0A0H2ZY91*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.34 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10MMM HEPES PH 7.0, 35% PEG 3350; MYAVA.00458.A.A1 PS00622 AT 60MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 20, 2010
RadiationMonochromator: Rigaku Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 42464 / Num. obs: 42081 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 27.38 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 22.15
Reflection shellResolution: 1.95→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3135 / Rsym value: 0.361 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb deposition 1c8u modified with ccp4 program chainsaw
Resolution: 1.95→36.05 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.671 / SU ML: 0.087 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.198 2152 5.1 %RANDOM
Rwork0.164 ---
all0.166 42464 --
obs0.166 42023 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.38 Å2
2--0.3 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4185 0 2 390 4577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224326
X-RAY DIFFRACTIONr_bond_other_d0.0010.022837
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9615933
X-RAY DIFFRACTIONr_angle_other_deg0.87736898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9465563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90722.732183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58115635
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4091538
X-RAY DIFFRACTIONr_chiral_restr0.0920.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214896
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02902
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_it0.8321.52782
X-RAY DIFFRACTIONr_mcbond_other0.2151.51105
X-RAY DIFFRACTIONr_mcangle_it1.50524488
X-RAY DIFFRACTIONr_scbond_it2.21231544
X-RAY DIFFRACTIONr_scangle_it3.4744.51438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 152 -
Rwork0.2 2786 -
obs-2955 94.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7914-0.0849-0.36961.03970.14450.7767-0.05310.0344-0.0096-0.0680.0471-0.0428-0.02880.03410.0060.027-0.0105-0.02030.0740.0020.040337.73221.01548.321
20.637-0.0344-0.24411.2164-0.04881.4059-0.0591-0.2145-0.02450.18920.06650.07520.031-0.1011-0.00740.04550.01760.0150.13420.01840.009825.94718.64672.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 281
2X-RAY DIFFRACTION1A300 - 301
3X-RAY DIFFRACTION1A285 - 521
4X-RAY DIFFRACTION2B1 - 282
5X-RAY DIFFRACTION2B285 - 439

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