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- PDB-6v3t: X-Ray Crystal Structure of Tribolium castaneum Arylalkylamine N-a... -

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Basic information

Entry
Database: PDB / ID: 6v3t
TitleX-Ray Crystal Structure of Tribolium castaneum Arylalkylamine N-acyltransferase in Complex with Acetyl-CoA
ComponentsDopamine N-acetyltransferase-like Protein
KeywordsTRANSFERASE / AANAT / Complex / CoA
Function / homologyN-acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / cytoplasm / Alpha Beta / ACETYL COENZYME *A / Dopamine N-acetyltransferase-like Protein
Function and homology information
Biological speciesTribolium castaneum (red flour beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsLewandowski, E.M. / Chen, Y.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Characterization of ArylalkylamineN-Acyltransferase fromTribolium castaneum: An Investigation into a Potential Next-Generation Insecticide Target.
Authors: O'Flynn, B.G. / Lewandowski, E.M. / Prins, K.C. / Suarez, G. / McCaskey, A.N. / Rios-Guzman, N.M. / Anderson, R.L. / Shepherd, B.A. / Gelis, I. / Leahy, J.W. / Chen, Y. / Merkler, D.J.
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dopamine N-acetyltransferase-like Protein
B: Dopamine N-acetyltransferase-like Protein
C: Dopamine N-acetyltransferase-like Protein
D: Dopamine N-acetyltransferase-like Protein
E: Dopamine N-acetyltransferase-like Protein
G: Dopamine N-acetyltransferase-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,16712
Polymers148,3096
Non-polymers4,8576
Water362
1
A: Dopamine N-acetyltransferase-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5282
Polymers24,7181
Non-polymers8101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dopamine N-acetyltransferase-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5282
Polymers24,7181
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dopamine N-acetyltransferase-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5282
Polymers24,7181
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dopamine N-acetyltransferase-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5282
Polymers24,7181
Non-polymers8101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Dopamine N-acetyltransferase-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5282
Polymers24,7181
Non-polymers8101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
G: Dopamine N-acetyltransferase-like Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5282
Polymers24,7181
Non-polymers8101
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.140, 131.660, 178.361
Angle α, β, γ (deg.)90.000, 90.050, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25G
16B
26C
17B
27D
18B
28E
19B
29G
110C
210D
111C
211E
112C
212G
113D
213E
114D
214G
115E
215G

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 1 - 213 / Label seq-ID: 1 - 213

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25GF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29GF
110CC
210DD
111CC
211EE
112CC
212GF
113DD
213EE
114DD
214GF
115EE
215GF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.500071, -0.865985, 0.000306), (-0.865985, -0.50007, 0.000374), (-0.000171, -0.000452, -1)50.826401, 88.16468, 416.208893

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Components

#1: Protein
Dopamine N-acetyltransferase-like Protein


Mass: 24718.213 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tribolium castaneum (red flour beetle) / Gene: TcasGA2_TC007905 / Production host: Escherichia coli (E. coli) / References: UniProt: D2A2Z2
#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.01 Å3/Da / Density % sol: 59.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 200mM Sodium Citrate, 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.84→89.18 Å / Num. obs: 41256 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.5
Reflection shellResolution: 2.84→2.96 Å / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4677

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FD6

4fd6


Resolution: 2.84→89.18 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.886 / SU B: 26.912 / SU ML: 0.475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.46
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3083 2052 4.9 %RANDOM
Rwork0.2352 ---
obs0.2385 39474 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.04 Å2 / Biso mean: 77.315 Å2 / Biso min: 44.68 Å2
Baniso -1Baniso -2Baniso -3
1-5.02 Å20 Å20.04 Å2
2--5.4 Å20 Å2
3----10.42 Å2
Refinement stepCycle: final / Resolution: 2.84→89.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10164 0 306 2 10472
Biso mean--73.78 64.83 -
Num. residues----1278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310738
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710015
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.68614521
X-RAY DIFFRACTIONr_angle_other_deg1.1641.60923258
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49551284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27122.442557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.508151927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0671566
X-RAY DIFFRACTIONr_chiral_restr0.0590.21386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211819
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022233
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1694TIGHT POSITIONAL0.160.11
1A1694TIGHT POSITIONAL0.150.11
1A1694TIGHT POSITIONAL0.140.11
1A1703TIGHT POSITIONAL0.160.11
1A1703TIGHT POSITIONAL0.160.11
1A1694TIGHT POSITIONAL0.150.11
1A1722TIGHT THERMAL2.261.12
2A1722TIGHT THERMAL2.291.12
3A1722TIGHT THERMAL2.381.12
4A1722TIGHT THERMAL2.281.12
5A1722TIGHT THERMAL2.411.12
6B1703TIGHT THERMAL2.391.12
7B1703TIGHT THERMAL2.231.12
8B1703TIGHT THERMAL2.211.12
9B1703TIGHT THERMAL2.481.12
10C1694TIGHT THERMAL2.321.12
11C1694TIGHT THERMAL2.361.12
12C1694TIGHT THERMAL2.311.12
13D1703TIGHT THERMAL2.291.12
14D1703TIGHT THERMAL2.341.12
15E1694TIGHT THERMAL2.241.12
LS refinement shellResolution: 2.84→2.914 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 152 -
Rwork0.391 2938 -
all-3090 -
obs--100 %

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