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- PDB-6art: Aspergillus fumigatus Cytosolic Thiolase: Apo enzyme in complex w... -

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Basic information

Entry
Database: PDB / ID: 6art
TitleAspergillus fumigatus Cytosolic Thiolase: Apo enzyme in complex with cesium ions
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / thiolase / Claisen Condensation / 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, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase ...Thiolase, conserved site / Thiolases signature 2. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / 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-CoA acetyltransferase erg10B, cytosolic
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
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 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_conn.ptnr2_symmetry

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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)166,44326
Polymers164,0314
Non-polymers2,41222
Water19,8171100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19250 Å2
ΔGint-603 kcal/mol
Surface area48580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.370, 105.290, 110.430
Angle α, β, γ (deg.)90.000, 108.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Acetyl-CoA acetyltransferase


Mass: 41007.848 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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1100 / 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: 2.4 Å3/Da / Density % sol: 48.69 % / Mosaicity: 0.33 °
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 21% PEG 3350, 0.1M CsCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.4586 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: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.25→67.46 Å / Num. obs: 73455 / % possible obs: 99.7 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.33 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.041 / Rrim(I) all: 0.112 / Net I/σ(I): 16.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.25-2.35.80.35143190.9260.1590.38795.6
11.02-67.466.60.0536600.9820.0230.05898.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.34 Å104.66 Å
Translation8.34 Å104.66 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: 2.25→56.91 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.34
RfactorNum. reflection% reflection
Rfree0.1927 3811 5.19 %
Rwork0.1522 --
obs0.1543 73451 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.99 Å2 / Biso mean: 34.323 Å2 / Biso min: 5.96 Å2
Refinement stepCycle: final / Resolution: 2.25→56.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11320 0 37 1100 12457
Biso mean--33.83 33.21 -
Num. residues----1582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711598
X-RAY DIFFRACTIONf_angle_d0.83415767
X-RAY DIFFRACTIONf_chiral_restr0.0531871
X-RAY DIFFRACTIONf_plane_restr0.0062081
X-RAY DIFFRACTIONf_dihedral_angle_d18.8114229
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
2.25-2.27560.23782680.21145544822
2.2756-2.30240.24842460.192845954841
2.3024-2.33040.22712560.185644724728
2.3304-2.35990.23782760.179545654841
2.3599-2.3910.20632020.175146684870
2.391-2.42370.23992660.176544794745
2.4237-2.45840.22162680.176146494917
2.4584-2.49510.21672320.168845644796
2.4951-2.53410.22072510.168945604811
2.5341-2.57560.1882450.165445634808
2.5756-2.620.20862180.158845924810
2.62-2.66770.22952060.175645774783
2.6677-2.7190.22412860.178845944880
2.719-2.77450.23652380.171646324870
2.7745-2.83480.21472420.165345454787
2.8348-2.90070.20813000.167144694769
2.9007-2.97330.19942460.1646054851
2.9733-3.05370.19682820.156745414823
3.0537-3.14350.19232160.162145514767
3.1435-3.2450.17832350.154346424877
3.245-3.36090.20392670.153545354802
3.3609-3.49550.18972880.155445134801
3.4955-3.65450.182180.148446234841
3.6545-3.84720.19262760.136545324808
3.8472-4.08810.17122870.129245364823
4.0881-4.40370.14072400.11846004840
4.4037-4.84660.13862000.113645974797
4.8466-5.54740.16322730.126945904863
5.5474-6.98720.19921670.143246384805
6.9872-56.92820.16853060.139344834789
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)
11.5353-0.2021-0.48690.83710.58442.0611-0.06530.19990.0834-0.4348-0.0547-0.4163-0.07980.55590.08890.42650.02440.14880.57430.00050.243810.2016-25.7016-60.6885
22.16910.0473-0.73981.36440.33051.0494-0.0761-0.2453-0.6494-0.1625-0.2214-0.32910.47090.4970.28040.40830.2210.0940.59470.15080.38326.6621-42.3905-42.7341
32.6772-0.6725-0.85494.4878-0.35362.706-0.1051-0.57220.24630.21010.3753-0.6414-0.05080.8084-0.27020.26430.08440.07981.07480.03150.618624.4839-28.6388-43.9607
41.91450.12120.23140.80980.59890.5756-0.15-0.1084-0.7618-0.4453-0.0386-0.49270.54380.96130.11560.60.32760.34930.82090.07780.537316.7067-42.5233-59.2488
51.68560.36870.35531.12180.0982.5479-0.12190.1172-0.0106-0.4529-0.10180.1092-0.0614-0.21920.2260.37430.06040.01060.3385-0.06520.1526-10.842-29.0559-59.964
62.2729-1.4492.30763.29940.33846.9926-0.19940.004-0.3148-0.47570.07650.77870.6167-0.7806-0.09280.3189-0.0518-0.10910.7477-0.19360.405-28.2354-36.3076-59.5086
72.43740.27540.6810.7737-0.36981.5819-0.19640.35890.4213-0.6786-0.08090.1226-0.295-0.37440.2650.67960.1242-0.12170.5274-0.0890.1874-15.7674-21.8779-70.4089
82.31361.3786-0.77320.8037-0.84834.86550.0542-0.10490.06730.05310.0262-0.1559-0.3743-0.0154-0.14420.10010.0633-0.06310.00090.01080.16292.1118-20.8304-1.0061
91.2995-0.03130.19020.60530.36250.7002-0.02890.11750.1106-0.06260.0476-0.1267-0.06440.0469-0.00930.1013-0.0065-0.00440.053-0.00940.1403-3.3886-18.1222-9.4656
101.9735-0.11830.22722.0666-0.26392.3544-0.12790.33540.2097-0.3140.1017-0.4737-0.02880.2001-0.01550.1309-0.06480.0340.1662-0.01940.281812.9648-13.708-13.3785
111.53880.3837-0.0751.4147-0.00320.5378-0.0075-0.16310.31340.1190.0239-0.1525-0.13710.0524-0.02310.14460.0005-0.03850.0731-0.04240.21340.7109-8.97883.0638
122.27210.4186-0.94172.50722.13162.4575-0.1226-0.0290.17030.0924-0.07430.19640.1123-0.17790.0580.06420.0728-0.01430.0860.02680.1145-29.3542-19.3896-8.6016
131.60060.22680.1230.61640.17270.8704-0.04410.13150.0003-0.1015-0.01240.0262-0.0178-0.07930.04460.0886-0.0011-0.0130.08470.01770.0729-21.142-24.5566-12.0461
143.513-0.5455-0.08093.84241.48544.3765-0.05760.62280.3802-0.42440.01090.1885-0.4713-0.2389-0.01850.15290.0346-0.0670.26030.07040.1681-38.553-18.6297-19.4856
152.09270.06360.12191.55480.45260.9914-0.0253-0.0889-0.19130.0414-0.01590.10830.0574-0.19670.04370.085-0.0178-0.00860.09350.01790.0913-30.7095-31.4978-3.9361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 124 )A4 - 124
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 196 )A125 - 196
3X-RAY DIFFRACTION3chain 'A' and (resid 197 through 235 )A197 - 235
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 398 )A236 - 398
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 196 )B0 - 196
6X-RAY DIFFRACTION6chain 'B' and (resid 197 through 224 )B197 - 224
7X-RAY DIFFRACTION7chain 'B' and (resid 225 through 398 )B225 - 398
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 28 )C1 - 28
9X-RAY DIFFRACTION9chain 'C' and (resid 29 through 195 )C29 - 195
10X-RAY DIFFRACTION10chain 'C' and (resid 196 through 256 )C196 - 256
11X-RAY DIFFRACTION11chain 'C' and (resid 257 through 398 )C257 - 398
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 28 )D1 - 28
13X-RAY DIFFRACTION13chain 'D' and (resid 29 through 195 )D29 - 195
14X-RAY DIFFRACTION14chain 'D' and (resid 196 through 224 )D196 - 224
15X-RAY DIFFRACTION15chain 'D' and (resid 225 through 398 )D225 - 398

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