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- PDB-3u0a: Crystal structure of an Acyl-CoA thioesterase II TesB2 from Mycob... -

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Basic information

Entry
Database: PDB / ID: 3u0a
TitleCrystal structure of an Acyl-CoA thioesterase II TesB2 from Mycobacterium marinum
ComponentsAcyl-CoA thioesterase II TesB2
KeywordsHYDROLASE / Structural Genomics / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Acyl-CoA thioesterase II
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 II TesB2
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsArakaki, T.L. / Staker, B.L. / Clifton, M.C. / Sankaran, B. / Seattle 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
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3May 25, 2016Group: Structure summary
Revision 1.4Sep 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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 TesB2
B: Acyl-CoA thioesterase II TesB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,90814
Polymers62,9792
Non-polymers93012
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-175 kcal/mol
Surface area19610 Å2
MethodPISA
2
A: Acyl-CoA thioesterase II TesB2
B: Acyl-CoA thioesterase II TesB2
hetero molecules

A: Acyl-CoA thioesterase II TesB2
B: Acyl-CoA thioesterase II TesB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,81628
Polymers125,9574
Non-polymers1,85924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area17970 Å2
ΔGint-367 kcal/mol
Surface area37390 Å2
MethodPISA
3
A: Acyl-CoA thioesterase II TesB2
B: Acyl-CoA thioesterase II TesB2
hetero molecules

A: Acyl-CoA thioesterase II TesB2
B: Acyl-CoA thioesterase II TesB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,81628
Polymers125,9574
Non-polymers1,85924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area17950 Å2
ΔGint-368 kcal/mol
Surface area37410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.130, 138.160, 81.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acyl-CoA thioesterase II TesB2


Mass: 31489.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: tesB2, MMAR_2095 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2HN47
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MymaA.00458.a at 47 mg/ml, 1% PEG 3350, 1000 mM ammonium sulfate, 25% PEG 3350 cryo, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 24, 2011
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 20168 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.506 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.560.4564.298181493100
2.56-2.640.4154.793981431100
2.64-2.710.3445.692081401100
2.71-2.80.2846.78902135399.9
2.8-2.890.2268.487341331100
2.89-2.990.18110.282541256100
2.99-3.10.1431381791249100
3.1-3.230.11515.97748118499.9
3.23-3.370.08819.875461151100
3.37-3.540.07423.471181097100
3.54-3.730.06826.26383103897.7
3.73-3.950.05431.3626598199.8
3.95-4.230.04237.96011934100
4.23-4.560.03941.65565872100
4.56-50.03742.2504880199.6
5-5.590.04536.5459173299.5
5.59-6.460.04534.6400665499.5
6.46-7.910.03440.1358656099.1
7.91-11.180.0258.1273044098.9
11.180.02453.9122721077.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.7 Å
Translation2.5 Å19.7 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1c8u

1c8u


Resolution: 2.5→19.91 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.878 / SU B: 16.874 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1022 5.1 %RANDOM
Rwork0.238 ---
obs0.241 20154 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.567 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å20 Å20 Å2
2--1.52 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 49 109 4033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194030
X-RAY DIFFRACTIONr_bond_other_d0.0010.022649
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.955490
X-RAY DIFFRACTIONr_angle_other_deg0.91136411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.223.191188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40115586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6851531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214550
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02853
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.475 59 -
Rwork0.402 1305 -
all-1364 -
obs--100 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8264-0.81010.29130.77980.86231.74110.0015-0.63240.08490.0573-0.0786-0.07390.1387-0.44130.07710.5219-0.04610.02630.68260.0180.36938.44117.71338.677
21.6719-0.35920.49650.1262-0.29420.92950.0227-0.20.1188-0.0340.01-0.03620.0303-0.0079-0.03270.5012-0.0048-0.00230.4896-0.04760.415733.62820.99127.709
38.4520.5591.60261.60891.8152.17020.3255-0.6852-0.55210.0101-0.1338-0.12350.0689-0.3067-0.19180.4675-0.13230.07280.65220.0710.40298.39213.23137.446
40.97760.11830.12080.84881.15811.83840.1098-0.0425-0.07450.2248-0.0436-0.0360.0837-0.2028-0.06620.4333-0.0180.0350.53680.00380.483416.93315.13332.753
53.1214-3.3893-0.35489.7103-2.00160.9904-0.5324-1.7807-0.89060.33740.72511.40710.07160.6644-0.19270.57040.13050.19181.28250.33990.717519.738-4.36627.329
60.19410.1972-0.52930.2052-0.55081.47850.04980.06870.0920.03330.08450.0501-0.0929-0.2409-0.13430.48890.00370.01520.5357-0.08670.513518.75816.79626.617
72.5539-2.3604-0.20195.24261.48081.1648-0.0813-0.1687-0.13820.14320.25180.07020.0039-0.008-0.17050.4437-0.07380.05350.43970.03440.459718.62711.61625.243
81.5250.49090.94020.35480.47360.7613-0.05780.3816-0.241-0.09390.06650.0186-0.11980.0712-0.00870.49090.0127-0.010.5671-0.02310.43838.29411.6414.311
92.14670.8004-0.76290.4065-0.51050.95520.03320.03420.03870.0766-0.1159-0.015-0.02940.04220.08270.48340.036-0.00530.4631-0.0270.428936.70914.04912.367
101.8937-0.94180.73950.921.01044.49910.2710.34810.2714-0.3568-0.4458-0.1008-0.5873-0.66610.17480.55760.17230.04330.68680.03910.443311.72620.742-0.683
116.0024-2.5508-3.4033.08293.34243.7980.5420.2970.04360.1871-0.4294-0.02060.2639-0.4202-0.11260.71510.1634-0.06430.5591-0.04170.271718.47915.3050.371
121.2512-1.3763-0.32181.84540.50610.2770.08890.1877-0.0926-0.47910.11530.1268-0.23080.0646-0.20420.6482-0.1449-0.02340.55610.03510.441523.01522.3237.217
131.1059-0.96860.11680.8588-0.09670.06940.04410.2470.0240.0587-0.17-0.02040.0776-0.10.12580.54730.03880.05490.5926-0.02960.441818.28719.6649.825
14111.3498-34.38431.87414.55338.031318.87813.09630.78412.2442-2.1988-0.5955-1.7618-2.6071-0.433-2.50091.00610.16020.45070.04620.05310.665221.96645.41815.354
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 31
2X-RAY DIFFRACTION2A32 - 122
3X-RAY DIFFRACTION3A123 - 160
4X-RAY DIFFRACTION4A161 - 207
5X-RAY DIFFRACTION5A208 - 215
6X-RAY DIFFRACTION6A216 - 252
7X-RAY DIFFRACTION7A253 - 276
8X-RAY DIFFRACTION8B1 - 59
9X-RAY DIFFRACTION9B60 - 117
10X-RAY DIFFRACTION10B118 - 161
11X-RAY DIFFRACTION11B162 - 183
12X-RAY DIFFRACTION12B184 - 229
13X-RAY DIFFRACTION13B230 - 271
14X-RAY DIFFRACTION14B272 - 278

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