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- PDB-5k18: The NatB Acetyltransferase Complex Bound To bisubstrate inhibitor -

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Basic information

Entry
Database: PDB / ID: 5k18
TitleThe NatB Acetyltransferase Complex Bound To bisubstrate inhibitor
Components
  • Bisubstrate inhibitor
  • N-terminal acetyltransferase B complex subunit NAT3
  • Uncharacterized protein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / N-terminal acetyltransferase complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
N-acetyltransferase B complex, non-catalytic subunit / N-acetyltransferase B complex (NatB) non catalytic subunit / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
COENZYME A / N-terminal acetyltransferase B complex subunit NAT3 / N-terminal acetyltransferase B complex subunit MDM20
Similarity search - Component
Biological speciesCandida albicans WO-1 (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsHong, H. / Cai, Y. / Zhang, S. / Han, A.
CitationJournal: Structure / Year: 2017
Title: Molecular Basis of Substrate Specific Acetylation by N-Terminal Acetyltransferase NatB
Authors: Hong, H. / Cai, Y. / Zhang, S. / Ding, H. / Wang, H. / Han, A.
History
DepositionMay 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_close_contact / struct_conn
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.0Apr 5, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine_hist / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_torsion.auth_seq_id / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: N-terminal acetyltransferase B complex subunit NAT3
C: Uncharacterized protein
D: N-terminal acetyltransferase B complex subunit NAT3
F: Bisubstrate inhibitor
E: Bisubstrate inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,8548
Polymers225,3196
Non-polymers1,5352
Water32418
1
A: Uncharacterized protein
B: N-terminal acetyltransferase B complex subunit NAT3
F: Bisubstrate inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4274
Polymers112,6603
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-20 kcal/mol
Surface area39300 Å2
MethodPISA
2
C: Uncharacterized protein
D: N-terminal acetyltransferase B complex subunit NAT3
E: Bisubstrate inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,4274
Polymers112,6603
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-26 kcal/mol
Surface area38320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.054, 91.087, 101.740
Angle α, β, γ (deg.)70.12, 88.91, 84.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized protein


Mass: 89468.242 Da / Num. of mol.: 2 / Fragment: UNP residues 53-745
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans WO-1 (yeast) / Strain: WO-1 / Gene: CAWG_01335 / Plasmid: pET-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C4YFL7
#2: Protein N-terminal acetyltransferase B complex subunit NAT3


Mass: 22003.117 Da / Num. of mol.: 2 / Fragment: UNP residues 2-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans WO-1 (yeast) / Strain: WO-1 / Gene: CAWG_00748 / Plasmid: pET-DUET / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C4YDZ9
#3: Protein/peptide Bisubstrate inhibitor


Mass: 1188.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOLECULAR

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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: 3.48 Å3/Da / Density % sol: 64.62 % / Mosaicity: 0.595 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: NaCl, PEG4000, glycerol,1,3-butanediol and DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.93911 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93911 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 90683 / % possible obs: 98.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 6.5
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.647 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K04

5k04


Resolution: 2.73→35.74 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 2000 2.88 %
Rwork0.187 --
obs0.189 69498 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14294 0 96 18 14408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914662
X-RAY DIFFRACTIONf_angle_d1.45519849
X-RAY DIFFRACTIONf_dihedral_angle_d5.098793
X-RAY DIFFRACTIONf_chiral_restr0.0642274
X-RAY DIFFRACTIONf_plane_restr0.0072480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7329-2.80120.363910.25113078X-RAY DIFFRACTION60
2.8012-2.87690.30911200.25354067X-RAY DIFFRACTION78
2.8769-2.96150.31981370.25694577X-RAY DIFFRACTION90
2.9615-3.0570.31671470.24845015X-RAY DIFFRACTION98
3.057-3.16620.31751520.23595082X-RAY DIFFRACTION99
3.1662-3.29290.29951490.21985035X-RAY DIFFRACTION99
3.2929-3.44270.27381500.21415058X-RAY DIFFRACTION99
3.4427-3.6240.28971510.19825099X-RAY DIFFRACTION99
3.624-3.85080.24951500.18095074X-RAY DIFFRACTION99
3.8508-4.14770.25781510.16085083X-RAY DIFFRACTION99
4.1477-4.56440.19951490.14925047X-RAY DIFFRACTION99
4.5644-5.22310.19381510.14825083X-RAY DIFFRACTION99
5.2231-6.57390.21521510.19315102X-RAY DIFFRACTION100
6.5739-35.74440.19581510.16155098X-RAY DIFFRACTION99
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)
10.0352-0.00670.0050.02470.02450.0230.17370.04470.36420.4233-0.0091-0.0499-0.72270.2980.00111.1329-0.1173-0.26651.1301-0.2361.592-14.20098.707915.7326
21.87282.04070.80592.28380.99830.57930.3825-0.1786-0.24180.3166-0.0843-0.69240.2110.8899-0.19720.4841-0.0323-0.17580.5012-0.01610.6749-26.3619-5.820413.4187
30.7762-0.09020.16692.0887-0.57291.45170.09210.2058-0.0075-0.3106-0.03380.42620.4779-0.1628-0.0680.33910.0016-0.1120.2721-0.00260.3835-58.08-14.0379-14.4283
40.80260.3631-0.1091.2451-0.06441.0014-0.00810.14860.0345-0.18410.04360.0125-0.14660.0719-0.07460.30320.0571-0.0060.2143-0.01270.1726-35.652619.1257-19.2628
51.87840.04520.51273.209-1.18911.14840.05650.1580.0002-0.00030.01940.2979-0.15290.0183-0.06940.25350.04050.00150.24-0.01570.2728-55.66870.7978-7.1755
61.7433-0.07970.11121.50170.11192.678-0.0607-0.1303-0.20580.2403-0.12530.59260.0505-0.43270.07950.28380.0390.01650.33530.00780.491-66.65440.9021-2.496
70.5096-0.08570.17711.2585-0.35330.43870.0364-0.13120.07730.39130.07020.8152-0.2465-0.5511-0.05860.43180.17430.15290.47830.03120.655-72.43666.68340.386
80.3648-0.4256-0.21592.60850.37545.0015-0.2031-0.16560.84370.3113-0.2118-0.124-0.7753-0.08790.16430.59380.0980.00390.4083-0.09280.7519-63.214723.69785.552
91.69570.09570.18880.0458-0.07960.2265-0.0178-0.11590.12940.29670.10250.1919-0.3463-0.38590.14430.4790.22490.21230.4343-0.00720.5811-72.78414.70666.6547
103.1870.8393-1.37764.256-1.14510.74770.3514-0.16610.1392-0.0747-0.31460.32280.1469-0.08030.05880.337-0.3177-0.05891.0194-0.0410.849-51.595129.42937.7344
111.47350.5114-0.37932.07270.27782.70140.0438-0.07690.06190.3059-0.04070.26550.1771-0.2351-0.07170.3614-0.08030.07010.3228-0.03630.2088-24.432744.837450.1244
120.65820.1038-0.6821.17920.38642.29470.1763-0.00930.1829-0.09530.0678-0.4919-0.59710.6337-0.24640.4109-0.22560.14230.6221-0.12880.52873.793461.458128.0709
130.7625-0.14610.37161.31590.12681.54530.08830.0510.0325-0.3419-0.03940.1798-0.1076-0.0478-0.06980.3005-0.01220.00260.1576-0.01970.2189-29.700744.42776.6349
141.85340.6888-0.2260.56390.50923.23250.0692-0.03880.0905-0.02840.0762-0.09520.04010.2128-0.150.1758-0.00680.02220.2832-0.04180.2171-11.01640.79931.1824
151.10270.532-0.08561.3895-0.24821.0909-0.0752-0.0408-0.34140.09390.1037-0.75030.30290.4017-0.03790.31150.1150.01220.4933-0.0660.51122.354529.121429.5936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 18 THROUGH 65 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 66 THROUGH 117 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 118 THROUGH 354 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 355 THROUGH 745 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 2 THROUGH 53 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 54 THROUGH 99 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 100 THROUGH 136 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 137 THROUGH 146 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 147 THROUGH 188 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 37 THROUGH 100 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 101 THROUGH 236 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 237 THROUGH 365 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 366 THROUGH 745 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 2 THROUGH 63 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 64 THROUGH 188 )

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