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- PDB-6aqp: Aspergillus fumigatus Cytosolic Thiolase: Acetylated enzyme in co... -

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Basic information

Entry
Database: PDB / ID: 6aqp
TitleAspergillus fumigatus Cytosolic Thiolase: Acetylated enzyme in complex with CoA and potassium ions
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / thiolase / Claisen condensation / reaction intermediate / monovalent cation binding
Function / homology
Function and homology information


ergosterol biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase ...Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / COENZYME A / : / Acetyl-CoA acetyltransferase erg10B, cytosolic
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
Model detailsCrystallized in the presence of acetyl-CoA, K+, and NH4+. 3 active sites contain Ac-Cys92+CoA: 1 ...Crystallized in the presence of acetyl-CoA, K+, and NH4+. 3 active sites contain Ac-Cys92+CoA: 1 site contains Ac-Cys92+Ac-CoA (alternate conformations).
AuthorsMarshall, A.C. / Bond, C.S. / Bruning, J.B.
CitationJournal: Acs Catalysis / Year: 2018
Title: Structure of Aspergillus fumigatus Cytosolic Thiolase: Trapped Tetrahedral Reaction Intermediates and Activation by Monovalent Cations
Authors: Marshall, A.C. / Bond, C.S. / Bruning, J.B.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
C: Acetyl-CoA acetyltransferase
D: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,92324
Polymers164,2004
Non-polymers3,72320
Water46,8932603
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22600 Å2
ΔGint-109 kcal/mol
Surface area48170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.370, 106.980, 111.090
Angle α, β, γ (deg.)90.000, 104.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Acetyl-CoA acetyltransferase


Mass: 41049.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_8G04000 / Plasmid: pET-57-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4WCL5, acetyl-CoA C-acetyltransferase

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Non-polymers , 5 types, 2623 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2603 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.5 Å3/Da / Density % sol: 50.88 % / Mosaicity: 0.86 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 23% PEG 3350, 0.2M AmS04, 0.2M KCl, 0.1M Bis-Tris pH 6.5

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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: Feb 25, 2017
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: 1.8→48.1 Å / Num. obs: 149532 / % possible obs: 95.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.27 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.053 / Rrim(I) all: 0.138 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.835.60.86866510.7020.3760.94990.4
9.86-48.16.40.0339020.9990.0140.03695

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.23 Å107.71 Å
Translation8.23 Å107.71 Å

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.17data scaling
PHASER2.5.7phasing
PHENIXdev_2747refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.907 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.36
RfactorNum. reflection% reflection
Rfree0.219 7583 5.07 %
Rwork0.1746 --
obs0.1769 149491 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.63 Å2 / Biso mean: 22.4351 Å2 / Biso min: 2.4 Å2
Refinement stepCycle: final / Resolution: 1.8→47.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11380 0 211 2606 14197
Biso mean--35.61 34.7 -
Num. residues----1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611866
X-RAY DIFFRACTIONf_angle_d0.85116163
X-RAY DIFFRACTIONf_chiral_restr0.0541898
X-RAY DIFFRACTIONf_plane_restr0.0062112
X-RAY DIFFRACTIONf_dihedral_angle_d20.194297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.82050.32892400.303747264966
1.8205-1.84190.32172640.298646904954
1.8419-1.86430.3032290.292447304959
1.8643-1.88790.30822270.288447444971
1.8879-1.91280.30032550.251247535008
1.9128-1.9390.29872340.254946734907
1.939-1.96670.26712200.22547374957
1.9667-1.9960.2552420.217647484990
1.996-2.02720.25222560.200647455001
2.0272-2.06050.20612690.193146624931
2.0605-2.0960.22452440.196347825026
2.096-2.13410.26452740.193146574931
2.1341-2.17520.24032500.183647434993
2.1752-2.21960.22762680.190546634931
2.2196-2.26780.26422700.219947034973
2.2678-2.32060.20422720.191247325004
2.3206-2.37860.24393060.178346814987
2.3786-2.44290.22532460.175746844930
2.4429-2.51480.22243080.16746965004
2.5148-2.5960.20732320.168747354967
2.596-2.68870.23592620.166247084970
2.6887-2.79640.22032320.162947544986
2.7964-2.92360.21062480.162447645012
2.9236-3.07770.22472400.156647524992
3.0777-3.27050.18162500.141347204970
3.2705-3.5230.19882360.134147655001
3.523-3.87740.16682390.130647645003
3.8774-4.43810.16662480.122347885036
4.4381-5.59020.14922590.126347675026
5.5902-47.92420.20542630.16148425105
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)
11.61330.3135-0.06420.66640.35823.022-0.080.09060.33440.05160.0280.0642-0.0477-0.11890.06020.14860.02630.00140.21160.06120.093531.637217.7675168.0417
20.9814-0.1528-0.62860.5908-0.07571.1515-0.06420.2198-0.0237-0.08150.0332-0.02670.08180.04520.02620.1623-0.0024-0.00490.31850.02460.089342.04199.8504159.6695
31.61080.16830.32341.1002-0.02121.6532-0.01990.3157-0.0852-0.12850.05320.07790.107-0.2341-0.0320.1371-0.0343-0.00140.3180.02310.087825.49772.8088162.4546
41.65831.4724-0.28032.1316-1.42492.8148-0.0125-0.1226-0.06610.1381-0.00420.0427-0.03680.1212-0.03550.12280.0773-0.00110.410.06060.146360.35536.5943171.216
50.9851-0.05530.10560.9107-0.28941.3265-0.02160.06620.11180.0232-0.0268-0.1376-0.07650.21250.0650.1412-0.0121-0.00580.29810.06060.113550.754114.6372164.6663
61.9796-0.21760.25950.96750.14011.1224-0.0703-0.24110.3630.07380.0443-0.1815-0.13420.43270.03340.1944-0.0579-0.05090.43950.00320.169363.443919.7793176.161
71.4004-0.5413-0.09321.03860.10991.9178-0.03490.1652-0.0618-0.0845-0.0012-0.03330.0072-0.11650.01480.0831-0.0124-0.0124-0.0504-0.00880.095144.622523.6115109.0754
80.9134-0.06290.01570.5799-0.23680.4701-0.0381-0.24870.06650.09490.01310.0382-0.0475-0.0290.01530.11890.01530.0056-0.0325-0.02680.092547.253232.9248121.0881
92.4519-0.28260.04884.8953-0.18832.6592-0.1389-0.2206-0.4832-0.0960.02110.03330.4248-0.01840.05390.04970.00220.01920.07240.03420.228329.233620.1338114.1864
100.9311-0.0655-0.06030.8578-0.05520.4755-0.0244-0.03040.1363-0.01440.01250.0686-0.1255-0.0575-0.00010.10910.0144-0.02360.007-0.00780.12440.572340.0449111.4623
110.86680.3087-0.91141.7261-1.06292.6293-0.02640.04330.1305-0.02740.0349-0.0462-0.0212-0.1402-0.03760.08180.0007-0.03790.0136-0.01240.105273.188431.0378118.4021
120.978-0.27370.29310.5282-0.01840.5349-0.093-0.4026-0.03970.08730.0885-0.0013-0.0026-0.02310.0140.0999-0.00260.0024-0.40370.04220.092264.362522.2994119.9357
131.99230.5711-0.1362.5907-0.39520.9521-0.0946-0.4426-0.07110.2890.0656-0.13020.01720.07880.01960.14160.0419-0.03020.06560.01620.092378.780415.5897127.8813
140.4755-0.12050.12640.9439-0.02980.3736-0.02890.14-0.0261-0.10240.0012-0.11310.05260.06320.01550.0967-0.00620.01230.0142-0.0010.12474.493720.1959107.7278
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 68 )A0 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 175 )A69 - 175
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 398 )A176 - 398
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 43 )B0 - 43
5X-RAY DIFFRACTION5chain 'B' and (resid 44 through 175 )B44 - 175
6X-RAY DIFFRACTION6chain 'B' and (resid 176 through 398 )B176 - 398
7X-RAY DIFFRACTION7chain 'C' and (resid 0 through 68 )C0 - 68
8X-RAY DIFFRACTION8chain 'C' and (resid 69 through 195 )C69 - 195
9X-RAY DIFFRACTION9chain 'C' and (resid 196 through 216 )C196 - 216
10X-RAY DIFFRACTION10chain 'C' and (resid 217 through 398 )C217 - 398
11X-RAY DIFFRACTION11chain 'D' and (resid 0 through 43 )D0 - 43
12X-RAY DIFFRACTION12chain 'D' and (resid 44 through 195 )D44 - 195
13X-RAY DIFFRACTION13chain 'D' and (resid 196 through 256 )D196 - 256
14X-RAY DIFFRACTION14chain 'D' and (resid 257 through 398 )D257 - 398

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