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

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Basic information

Entry
Database: PDB / ID: 6arr
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: 1.822 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
Water25,7611430
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19280 Å2
ΔGint-604 kcal/mol
Surface area48520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.410, 105.270, 110.450
Angle α, β, γ (deg.)90.000, 108.610, 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.: 1430 / 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: 48.72 % / Mosaicity: 0.37 °
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: 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: 1.82→56.93 Å / Num. obs: 137982 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 18.74 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.09 / Rrim(I) all: 0.248 / Net I/σ(I): 8.3 / Num. measured all: 1019921 / Scaling rejects: 248
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.82-1.856.82.1514562867520.3140.8852.33199.4
9.98-56.936.50.04457418770.9970.0180.04831.798.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.26 Å104.67 Å
Translation8.26 Å104.67 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: 1.822→56.927 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.86
RfactorNum. reflection% reflection
Rfree0.2086 6801 4.93 %
Rwork0.1772 --
obs0.1787 137982 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.58 Å2 / Biso mean: 32.9606 Å2 / Biso min: 7.18 Å2
Refinement stepCycle: final / Resolution: 1.822→56.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11324 0 37 1430 12791
Biso mean--31.88 35.89 -
Num. residues----1582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811638
X-RAY DIFFRACTIONf_angle_d0.84415827
X-RAY DIFFRACTIONf_chiral_restr0.0561877
X-RAY DIFFRACTIONf_plane_restr0.0072089
X-RAY DIFFRACTIONf_dihedral_angle_d19.534261
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
1.822-1.84270.36232470.342443494596
1.8427-1.86440.34422240.316642994523
1.8644-1.88710.33572500.303843794629
1.8871-1.9110.31252410.284743144555
1.911-1.93620.2872520.27443604612
1.9362-1.96270.29542060.257343434549
1.9627-1.99070.25791770.242444284605
1.9907-2.02040.24462310.2443604591
2.0204-2.0520.2692420.233443524594
2.052-2.08570.27282170.226443514568
2.0857-2.12160.24622220.226343594581
2.1216-2.16020.22942220.215543634585
2.1602-2.20180.21822120.197843744586
2.2018-2.24670.22572410.18943724613
2.2467-2.29560.21421820.183243704552
2.2956-2.3490.18212440.179943824626
2.349-2.40770.2172570.170843164573
2.4077-2.47280.2252630.177543334596
2.4728-2.54560.22591910.174144194610
2.5456-2.62770.18742380.169643374575
2.6277-2.72160.17972130.166143864599
2.7216-2.83060.17972210.162444044625
2.8306-2.95940.22262090.161243724581
2.9594-3.11540.19142630.160443484611
3.1154-3.31060.19452000.154544014601
3.3106-3.56620.19232300.151944034633
3.5662-3.9250.16832110.134644014612
3.925-4.49280.15512250.123143984623
4.4928-5.65960.1642180.134144294647
5.6596-56.95490.18012520.151544794731
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)
11.54290.0601-0.48460.9059-0.39981.5749-0.0708-0.0556-0.14390.3113-0.05720.28380.119-0.4240.13310.33-0.06520.10090.48770.00610.2097-5.435219.4687264.0207
22.1294-0.6823-0.78212.04650.35811.6652-0.1460.5368-0.1539-0.18780.25450.42570.1478-0.6169-0.10020.3-0.22990.14641.1198-0.18580.6687-24.223115.1557253.8127
31.206-0.06410.19260.5252-0.34260.349-0.0008-0.0054-0.71530.40550.02050.51060.4032-0.68690.05770.5425-0.40350.49780.8146-0.07640.4535-15.84817.4044268.3976
41.3922-0.36280.35930.7088-0.04992.1182-0.1281-0.10230.00410.4073-0.0926-0.0947-0.03540.21210.22530.4007-0.05620.01230.37220.06460.158511.730720.9733269.2766
53.20680.92291.5482.94780.05065.3677-0.15520.3779-0.33590.36930.2436-0.55920.47160.6152-0.18150.29750.0268-0.15830.72260.14140.337329.179813.6006268.847
61.8072-0.37080.67860.5640.11121.3657-0.1984-0.33510.33980.6699-0.0636-0.1515-0.32850.39960.23710.67-0.1117-0.10770.53230.09430.198816.623828.1065279.7269
72.7595-1.3289-1.37110.62190.78695.87450.12860.07760.1318-0.04860.09730.1984-0.3412-0.0148-0.23320.0688-0.0569-0.0505-0.0136-0.00340.1215-1.212229.1062210.3598
81.1590.00670.07620.5299-0.27420.6686-0.0366-0.12550.10390.04820.03870.104-0.0752-0.03-0.00240.09730.0124-0.00630.04980.00040.12244.169531.8453218.7953
91.803-0.02340.15842.17470.57772.1967-0.0955-0.31810.19960.21160.08590.282-0.1022-0.2087-0.0120.12440.05690.02320.15280.01480.248-12.202736.3901222.8319
101.0705-0.3215-0.09651.2682-0.05180.3901-0.0260.13910.2831-0.08910.02780.128-0.1252-0.0434-0.00520.1296-0.0034-0.0360.080.03910.19960.199240.9676206.288
112.3788-0.506-0.48992.3918-2.0132.0417-0.09390.05410.1517-0.07210.0356-0.14430.22450.1120.02990.0534-0.0746-0.02940.0939-0.02540.083330.285930.5661217.9455
121.4236-0.1850.11030.7231-0.11180.7415-0.0528-0.12530.00050.06690.0104-0.0163-0.00650.04960.03610.08380.0029-0.00790.0754-0.00520.064322.06625.3919221.4011
133.63040.3919-0.26493.5972-1.89463.5129-0.0403-0.59050.45570.501-0.0022-0.191-0.36180.22-0.02590.1559-0.0092-0.07170.2387-0.06820.167239.483231.3219228.8228
141.5173-0.13910.15811.2071-0.0520.8294-0.03030.0735-0.131-0.0434-0.0046-0.10450.08970.16290.03060.07190.0149-0.00210.0954-0.00710.098931.638918.4479213.2776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 175 )A4 - 175
2X-RAY DIFFRACTION2chain 'A' and (resid 176 through 234 )A176 - 234
3X-RAY DIFFRACTION3chain 'A' and (resid 235 through 398 )A235 - 398
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 196 )B0 - 196
5X-RAY DIFFRACTION5chain 'B' and (resid 197 through 224 )B197 - 224
6X-RAY DIFFRACTION6chain 'B' and (resid 225 through 398 )B225 - 398
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 28 )C1 - 28
8X-RAY DIFFRACTION8chain 'C' and (resid 29 through 195 )C29 - 195
9X-RAY DIFFRACTION9chain 'C' and (resid 196 through 256 )C196 - 256
10X-RAY DIFFRACTION10chain 'C' and (resid 257 through 398 )C257 - 398
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 28 )D1 - 28
12X-RAY DIFFRACTION12chain 'D' and (resid 29 through 195 )D29 - 195
13X-RAY DIFFRACTION13chain 'D' and (resid 196 through 224 )D196 - 224
14X-RAY DIFFRACTION14chain 'D' and (resid 225 through 398 )D225 - 398

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