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- PDB-3ss6: Crystal structure of the Bacillus anthracis acetyl-CoA acetyltran... -

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Basic information

Entry
Database: PDB / ID: 3ss6
TitleCrystal structure of the Bacillus anthracis acetyl-CoA acetyltransferase
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / Alpha Beta / 3-Layer(aba)Sandwich / acetyl-CoA acetyltransferase
Function / homology
Function and homology information


acetyl-CoA C-acetyltransferase / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Thiolase, active site / Thiolases active site. / 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 ...Thiolase, active site / Thiolases active site. / 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 / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of the Bacillus anthracis acetyl-CoA acetyltransferase
Authors: Anderson, S.M. / Wawrzak, Z. / Onopriyenko, O. / Peterson, S.N. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,35212
Polymers84,5622
Non-polymers79010
Water18,3931021
1
A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
hetero molecules

A: Acetyl-CoA acetyltransferase
B: Acetyl-CoA acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,70424
Polymers169,1254
Non-polymers1,57920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area18520 Å2
ΔGint-261 kcal/mol
Surface area50020 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-116 kcal/mol
Surface area27340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.720, 94.720, 189.260
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-693-

HOH

21B-549-

HOH

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Components

#1: Protein Acetyl-CoA acetyltransferase


Mass: 42281.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS3932, BA_4240, GBAA_4240 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81MK7, UniProt: A0A6H3AND8*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7
Details: 2.5M Ammonium Sulfate, 100mM Bis-Tris Propane, pH 7, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2011 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 107991 / Num. obs: 107775 / % possible obs: 99.8 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 3.4 / Redundancy: 10.6 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 27.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.4 / Num. unique all: 10649 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→34.4 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9034 / SU ML: 0.4 / σ(F): 1.84 / σ(I): 3.4 / Phase error: 16.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1747 5385 5 %random
Rwork0.1523 ---
all0.1535 108045 --
obs0.1534 107678 99.7 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.093 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 111.88 Å2 / Biso mean: 25.52 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.0118 Å20 Å2-0 Å2
2--2.0118 Å20 Å2
3----4.0237 Å2
Refinement stepCycle: LAST / Resolution: 1.7→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5891 0 38 1021 6950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076123
X-RAY DIFFRACTIONf_angle_d1.1988320
X-RAY DIFFRACTIONf_chiral_restr0.085961
X-RAY DIFFRACTIONf_plane_restr0.0051093
X-RAY DIFFRACTIONf_dihedral_angle_d14.492295
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.2572 520 -
Rwork0.224 10057 -
all-3435 -
obs-3435 98.7 %
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)
10.43330.21550.11550.39470.01530.7036-0.01140.00860.0304-0.04460.02130.0241-0.05330.0144-0.02170.0795-0.0102-0.00160.05350.00220.105228.2995-17.13512.9384
20.9565-0.38110.03141.27390.13790.7918-0.03150.1998-0.0738-0.07890.00830.25910.1298-0.1736-0.04830.0878-0.0307-0.03440.1102-0.0010.134614.446-18.9478-2.3953
35.2525-1.50270.72923.3887-1.77341.4869-0.0542-0.36660.21450.32830.1780.4872-0.1856-0.2941-0.07960.14150.040.02170.2006-0.00580.24615.4654-6.40048.6019
41.692-0.128-0.01541.2580.04711.0889-0.03590.10160.2174-0.06130.0446-0.0067-0.16960.0156-0.02740.1311-0.0332-0.00950.09390.02380.125329.6167-5.7852-1.2255
51.63260.4482-0.05251.4871-0.48021.1479-0.0437-0.05670.0876-0.01240.0635-0.0656-0.22430.05470.00250.1141-0.04820.00020.1194-0.04990.098642.4682-9.191230.9765
60.7580.1417-0.20560.39040.0051.2483-0.0207-0.2065-0.00660.04330.0018-0.0676-0.05210.23350.030.0407-0.0165-0.00780.1033-0.00830.068237.9805-16.235528.5325
70.64780.2083-0.16933.4442-0.9821.4212-0.0537-0.2606-0.0305-0.0152-0.0157-0.11380.11920.32380.07810.0785-0.0077-0.01240.20180.0060.110946.1404-20.373236.1621
80.7577-0.52470.1091.307-0.2291.29670.032-0.1477-0.0866-0.1012-0.0468-0.18180.0310.4111-0.01680.0969-0.03320.00710.28480.00620.171655.1609-18.443825.6749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:170)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 171:223)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 224:249)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 250:391)A0
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:25)B0
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:212)B0
7X-RAY DIFFRACTION7chain 'B' and (resseq 213:265)B0
8X-RAY DIFFRACTION8chain 'B' and (resseq 266:391)B0

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