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

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Basic information

Entry
Database: PDB / ID: 6arg
TitleAspergillus fumigatus Cytosolic Thiolase: Apo enzyme in complex with rubidium 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
RUBIDIUM ION / Acetyl-CoA acetyltransferase erg10B, cytosolic
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.782 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 22, 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.ptnr3_auth_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

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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)165,56124
Polymers164,0314
Non-polymers1,52920
Water29,2741625
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18750 Å2
ΔGint-234 kcal/mol
Surface area48630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.260, 105.370, 110.260
Angle α, β, γ (deg.)90.000, 108.690, 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-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / 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.: 1625 / 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: 2.39 Å3/Da / Density % sol: 48.55 % / Mosaicity: 0.8 °
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 24% PEG 3350, 0.15M RbCl

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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: 1.78→36.2 Å / Num. obs: 144987 / % possible obs: 98.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.77 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.071 / Rrim(I) all: 0.183 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.78-1.815.51.67569820.3420.7751.85296.6
9.76-36.166.40.0489240.9970.020.05297.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.18 Å45.08 Å
Translation8.18 Å45.08 Å

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.5.17data scaling
PHASER2.5.7phasing
PHENIXdev_2686refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.782→36.2 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.28
RfactorNum. reflection% reflection
Rfree0.2199 7323 5.06 %
Rwork0.1819 --
obs0.1838 144843 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.66 Å2 / Biso mean: 32.843 Å2 / Biso min: 6.98 Å2
Refinement stepCycle: final / Resolution: 1.782→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11328 0 35 1625 12988
Biso mean--30.53 37.45 -
Num. residues----1582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711638
X-RAY DIFFRACTIONf_angle_d0.8515824
X-RAY DIFFRACTIONf_chiral_restr0.0561876
X-RAY DIFFRACTIONf_plane_restr0.0062088
X-RAY DIFFRACTIONf_dihedral_angle_d15.7267118
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.782-1.80220.3122290.30694390461996
1.8022-1.82340.33992310.29394544477597
1.8234-1.84570.30312310.28414491472297
1.8457-1.8690.32112070.27474580478797
1.869-1.89360.31352330.28614454468798
1.8936-1.91960.49271970.44744561475897
1.9196-1.9470.36312680.34764499476797
1.947-1.97610.27532270.23854530475798
1.9761-2.00690.24981840.22124636482098
2.0069-2.03980.25542880.21194509479798
2.0398-2.0750.26292430.22544542478598
2.075-2.11270.23042770.20034533481099
2.1127-2.15340.2332300.19494644487499
2.1534-2.19730.22672770.18834524480199
2.1973-2.24510.33932360.25724631486799
2.2451-2.29730.31962830.29084514479798
2.2973-2.35470.21252890.17494528481799
2.3547-2.41840.19962760.16614566484299
2.4184-2.48950.21752490.16594582483199
2.4895-2.56990.20022540.16184629488399
2.5699-2.66170.21932350.16674571480699
2.6617-2.76820.22422260.16054682490899
2.7682-2.89420.20232650.164571483699
2.8942-3.04670.18792030.159347174920100
3.0467-3.23750.18452630.153146244887100
3.2375-3.48720.18552400.144546454885100
3.4872-3.83780.1752350.138846884923100
3.8378-4.39230.16882450.124147064951100
4.3923-5.53070.15462470.123847144961100
5.5307-36.22640.16672550.13854715497099
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)
11.59670.07-0.19190.803-0.23411.0575-0.0530.0998-0.12060.1798-0.05050.31810.1038-0.55120.07560.2562-0.05260.08790.5331-0.00210.2434-44.285216.9758157.8367
22.1685-0.5598-0.45713.59310.59451.4019-0.08960.5618-0.1353-0.35610.22610.51690.0175-0.5258-0.11640.2929-0.10540.05730.9649-0.08840.49-56.358614.7641146.3824
31.39730.1409-0.130.402-0.38930.3993-0.0247-0.2116-0.6430.39570.05260.41990.4292-0.88890.2640.4277-0.21790.2430.84330.0250.4549-52.8797.7063166.6062
41.4272-0.31410.32130.83270.02362.0344-0.0704-0.06610.00470.2947-0.0875-0.091-0.01420.19180.13640.2726-0.04140.01780.35850.06150.1379-24.667120.2608164.3011
52.37640.09060.44741.1970.06041.7325-0.0844-0.21280.31080.5106-0.1215-0.1814-0.20320.42970.170.4309-0.0791-0.06450.50440.09260.1255-18.126725.4397173.3226
61.4551-0.77170.36060.86140.58131.46390.02220.05230.1411-0.06170.05810.0722-0.21360.0861-0.17540.0969-0.0376-0.01990.04710.01880.1455-37.506128.4631105.4522
71.33950.01760.20030.5292-0.21760.5241-0.0459-0.09820.13740.04640.04950.122-0.0739-0.037-0.00890.10720.01620.00770.0460.00280.1344-31.989231.1919113.9182
81.56220.03920.20291.64240.69341.8348-0.1074-0.29710.18330.19080.17440.2792-0.1133-0.1346-0.06150.16320.06820.04790.17060.01380.2676-48.469235.7714117.9197
91.3425-0.2030.05221.0147-0.06720.4826-0.03190.1370.2908-0.09450.03470.1174-0.1302-0.0356-0.03170.14790.0016-0.02330.07810.04860.2125-36.100340.3011101.344
101.6451-0.356-0.06991.6898-0.39490.1128-0.10040.06380.119-0.06960.0179-0.1140.02040.0597-0.00590.0782-0.0449-0.00570.1262-0.01610.0823-5.961429.9379113.027
111.487-0.12660.11260.4952-0.10370.6617-0.0479-0.1264-0.00170.05470.02410.0106-0.00940.0720.01590.09960.01040.00460.0874-0.00480.0775-14.219624.7696116.4979
122.97890.622-0.1762.9548-2.02072.9583-0.0566-0.45290.3640.3888-0.0248-0.0834-0.32520.1281-0.06710.1639-0.0024-0.06290.2407-0.06330.18463.220730.7478123.8578
131.5752-0.18380.11080.9386-0.0510.7954-0.03730.0741-0.1118-0.03870.0083-0.07050.07260.15510.03050.09060.01730.00890.1052-0.00640.1102-4.637117.8409108.4432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 196 )A4 - 196
2X-RAY DIFFRACTION2chain 'A' and (resid 197 through 256 )A197 - 256
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 398 )A257 - 398
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 196 )B0 - 196
5X-RAY DIFFRACTION5chain 'B' and (resid 197 through 398 )B197 - 398
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 28 )C1 - 28
7X-RAY DIFFRACTION7chain 'C' and (resid 29 through 195 )C29 - 195
8X-RAY DIFFRACTION8chain 'C' and (resid 196 through 256 )C196 - 256
9X-RAY DIFFRACTION9chain 'C' and (resid 257 through 398 )C257 - 398
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 28 )D1 - 28
11X-RAY DIFFRACTION11chain 'D' and (resid 29 through 195 )D29 - 195
12X-RAY DIFFRACTION12chain 'D' and (resid 196 through 224 )D196 - 224
13X-RAY DIFFRACTION13chain 'D' and (resid 225 through 398 )D225 - 398

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