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- PDB-3svk: Crystal structure of Acetyl-CoA acetyltransferase from Mycobacter... -

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Basic information

Entry
Database: PDB / ID: 3svk
TitleCrystal structure of Acetyl-CoA acetyltransferase from Mycobacterium avium
ComponentsAcetyl-CoA acetyltransferase
KeywordsTRANSFERASE / SSGCID / NIH / NIAID / SBRI / UW / Emerald BioStructures / Structural Genomics / 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, C-terminal / Thiolase, C-terminal domain / Thiolase / 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, 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 speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 13, 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 / 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 / _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)85,9433
Polymers85,9072
Non-polymers351
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-17 kcal/mol
Surface area26750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.310, 98.330, 151.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 4 / Auth seq-ID: 1 - 403 / Label seq-ID: 1 - 403

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Acetyl-CoA acetyltransferase


Mass: 42953.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_0980 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0QBF2, UniProt: A0A0H2ZTN6*PLUS, acetyl-CoA C-acetyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Internal tracking number 220558g1. PACT G1. 0.2 M sodium fluoride, 0.1 M Bis Tris propane, pH 7.5, 20% PEG3350. MyavA.00781.a.A1 PW28926 at 28 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2011
RadiationMonochromator: Asymmetric curved crystal, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.2→47.541 Å / Num. all: 42089 / Num. obs: 40680 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 39.668 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.262.50.3423.312939509086.3
2.26-2.320.4182.415895515690.5
2.32-2.390.2833.517618553998.7
2.39-2.460.251417083538999.5
2.46-2.540.214.616596518199.3
2.54-2.630.1655.716180505599.2
2.63-2.730.1616.514751486298.3
2.73-2.840.1177.914866464499.8
2.84-2.970.0959.214603454099.6
2.97-3.110.07711.213685427499.5
3.11-3.280.06213.613070411399.6
3.28-3.480.05815.211432382598.7
3.48-3.720.0491710363352796.8
3.72-4.020.04419.39637328095.7
4.02-4.40.03922.19651310099.7
4.4-4.920.03522.98797285399.8
4.92-5.680.03821.47730247299.7
5.68-6.960.03621.46518211299.5
6.96-9.840.02825.75213161899.8
9.840.02727.9286689598.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.54 Å
Translation2.5 Å47.54 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GOA

3goa


Resolution: 2.2→47.541 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 14.246 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.301 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2053 5 %RANDOM
Rwork0.24 ---
obs0.242 40680 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.489 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5167 0 1 165 5333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215234
X-RAY DIFFRACTIONr_bond_other_d0.0010.023349
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9697115
X-RAY DIFFRACTIONr_angle_other_deg0.93938178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335707
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82323.96202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06515785
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6771538
X-RAY DIFFRACTIONr_chiral_restr0.0820.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021015
X-RAY DIFFRACTIONr_mcbond_it0.6361.53533
X-RAY DIFFRACTIONr_mcbond_other0.151.51486
X-RAY DIFFRACTIONr_mcangle_it1.13425561
X-RAY DIFFRACTIONr_scbond_it1.74831701
X-RAY DIFFRACTIONr_scangle_it2.7574.51554
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4212 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.20.5
MEDIUM THERMAL0.432
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 130 -
Rwork0.527 2440 -
all-2570 -
obs--83.85 %
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)
12.07010.9508-0.26333.19820.34753.526-0.1565-0.0896-0.0371-0.54070.1799-0.37920.18630.3406-0.02340.26410.01010.05570.2281-0.01030.052235.01421.67164.905
23.198-0.67840.67751.2312-0.17132.5585-0.2221-0.23630.3362-0.02170.16850.1684-0.1301-0.23650.05360.1758-0.0037-0.04830.3291-0.01350.098814.78732.12577.947
31.5105-0.1501-0.51092.07820.22392.2523-0.1287-0.0868-0.1062-0.27750.07940.18670.3668-0.27180.04930.3025-0.0772-0.04330.24850.02040.037318.38716.91269.706
41.7411-1.0545-0.03843.4628-0.42793.5228-0.0830.0949-0.07570.55710.11850.46920.1539-0.3423-0.03560.2402-0.01410.0490.21610.00770.078719.24321.41839.593
53.2960.23110.71511.37980.17312.3081-0.27430.28550.38560.00950.1896-0.1862-0.18190.33030.08470.1775-0.0101-0.05650.34840.03010.102739.6832.23726.696
61.61820.0199-0.33621.9934-0.5182.4877-0.03240.0938-0.10360.2266-0.0237-0.14860.33320.34370.05610.26490.0732-0.05760.2324-0.01580.048536.08416.87834.922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 122
2X-RAY DIFFRACTION2A134 - 255
3X-RAY DIFFRACTION3A256 - 403
4X-RAY DIFFRACTION4B3 - 122
5X-RAY DIFFRACTION5B134 - 255
6X-RAY DIFFRACTION6B256 - 402

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