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- PDB-6bn2: Crystal structure of Acetyl-CoA acetyltransferase from Elizabethk... -

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Basic information

Entry
Database: PDB / ID: 6bn2
TitleCrystal structure of Acetyl-CoA acetyltransferase from Elizabethkingia anophelis NUHP1
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / SSGCID / Structural Genomics / Elizabethkingia anophelis / Acetyl-CoA acetyltransferase / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / 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
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Acetyl-CoA acetyltransferase from Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6026
Polymers42,3541
Non-polymers2485
Water8,647480
1
A: Acetyl-CoA acetyltransferase
hetero molecules

A: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,20412
Polymers84,7092
Non-polymers49610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area6080 Å2
ΔGint-70 kcal/mol
Surface area25940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.170, 167.420, 72.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-402-

CA

21A-403-

CA

31A-576-

HOH

41A-718-

HOH

51A-772-

HOH

61A-773-

HOH

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Components

#1: Protein Acetyl-CoA acetyltransferase


Mass: 42354.352 Da / Num. of mol.: 1 / Fragment: ElanA.00654.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_2261 / Plasmid: ElanA.00654.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3)
References: UniProt: A0A077EEP0, acetyl-CoA C-acetyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18.9 mg/mL ElanA.00654.a.B1.PS38241 + 3 mM AcetylCoA + RigakuReagents JCSG+ screen, E11: 14.5% w/v PEG8000, 20% w/v glycerol, 160 mM calcium acetate, 100 mM cacodylate/HCl, pH 6.5, ...Details: 18.9 mg/mL ElanA.00654.a.B1.PS38241 + 3 mM AcetylCoA + RigakuReagents JCSG+ screen, E11: 14.5% w/v PEG8000, 20% w/v glycerol, 160 mM calcium acetate, 100 mM cacodylate/HCl, pH 6.5, cryoprotectant: direct, tray 291032e11, puck DYA4-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 12, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→40.939 Å / Num. obs: 72724 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.028 % / Biso Wilson estimate: 17.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.057 / Χ2: 1.06 / Net I/σ(I): 20.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.695.0990.5113.0653250.860.57100
1.69-1.745.9940.4254.1452140.9260.465100
1.74-1.796.1910.3285.4850320.9570.358100
1.79-1.846.180.2567.0749160.9710.28100
1.84-1.916.20.1979.0647800.9830.216100
1.91-1.976.2020.15411.4245840.9890.168100
1.97-2.056.1950.11914.644760.9930.13100
2.05-2.136.2060.09717.643190.9950.10699.9
2.13-2.226.180.08320.4240820.9960.09199.9
2.22-2.336.1650.06824.0339640.9970.07599.9
2.33-2.466.1540.06126.4737320.9970.06799.9
2.46-2.616.1250.05329.6835830.9980.05899.8
2.61-2.796.070.04732.8233240.9980.05299.8
2.79-3.016.0650.04137.1631270.9980.04599.7
3.01-3.35.9880.03740.9728920.9990.0499.9
3.3-3.695.9210.03145.526110.9990.03499.8
3.69-4.265.8820.02848.6123310.9990.0399.4
4.26-5.225.9150.02550.4419770.9990.02899.7
5.22-7.385.810.02748.8315540.9990.02999.6
7.38-40.9395.4520.02350.189010.9990.02597.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LSQ per MorDa

3lsq


Resolution: 1.65→40.939 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.55
RfactorNum. reflection% reflectionSelection details
Rfree0.1561 2019 2.78 %0
Rwork0.1384 ---
obs0.1389 72721 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.6 Å2 / Biso mean: 24.0135 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 1.65→40.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 10 498 3367
Biso mean--47.23 38.74 -
Num. residues----393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69130.21531260.200650175143100
1.6913-1.7370.22231490.181650135162100
1.737-1.78810.18021700.162849405110100
1.7881-1.84580.16291330.156150355168100
1.8458-1.91180.17551630.150449925155100
1.9118-1.98840.16541110.140650665177100
1.9884-2.07880.15861650.136449965161100
2.0788-2.18840.16031490.135949925141100
2.1884-2.32550.14041620.13350345196100
2.3255-2.50510.14781420.136350515193100
2.5051-2.75710.17051350.140150575192100
2.7571-3.1560.15611120.136951255237100
3.156-3.97570.13491410.12851255266100
3.9757-40.95160.15061610.12935259542099
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)
11.4669-0.3486-0.34282.2414-0.22761.63650.0399-0.1815-0.04430.05350.0109-0.0092-0.01070.0717-0.04070.0938-0.0235-0.02440.14760.00980.08372.0841-28.520416.6093
20.63340.06-0.02830.8096-0.15880.84140.0516-0.0701-0.01950.0103-0.03-0.0318-0.02620.105-0.01260.0833-0.0097-0.00480.0921-0.00610.08644.5763-25.9716.0468
32.37540.2697-1.93961.2126-0.80543.46950.13640.18580.0941-0.0163-0.00350.255-0.1038-0.4693-0.1470.18920.0390.00910.2242-0.01590.2367-19.995-18.82137.5236
49.4031-2.08223.5891.4155-0.50562.8155-0.0575-0.61-0.07140.12280.12410.1958-0.2039-0.3105-0.06610.1967-0.03120.04070.2323-0.01840.1535-15.93-24.051328.3613
52.7638-0.89460.51273.04870.1832.18440.0585-0.39330.33780.2533-0.0663-0.4547-0.35810.40440.00280.2404-0.1034-0.03670.3036-0.03260.17436.1323-22.331826.7968
63.7571-1.1077-0.39283.36260.05283.7284-0.029-0.41530.54610.2021-0.02530.2539-0.522-0.27520.0470.2989-0.0060.05230.2181-0.07310.2953-17.1732-14.514122.7157
71.3240.1203-0.24450.63680.00171.18040.0468-0.1375-0.13360.0809-0.05190.0620.0851-0.04330.00270.133-0.0299-0.01130.12570.02290.1265-9.293-37.306616.1141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 140 )A26 - 140
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 170 )A141 - 170
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 190 )A171 - 190
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 217 )A191 - 217
6X-RAY DIFFRACTION6chain 'A' and (resid 218 through 250 )A218 - 250
7X-RAY DIFFRACTION7chain 'A' and (resid 251 through 393 )A251 - 393

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