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- PDB-8iym: Crystal structure of a protein acetyltransferase, HP0935 -

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Entry
Database: PDB / ID: 8iym
TitleCrystal structure of a protein acetyltransferase, HP0935
ComponentsN-acetyltransferase domain-containing protein
KeywordsTRANSFERASE / GNAT domain / protein acetyltransferase
Function / homologyacyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / : / THIOCYANATE ION / N-acetyltransferase domain-containing protein
Function and homology information
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDadireddy, V. / Mahanta, P. / Kumar, A. / Desirazu, R.N. / Ramakumar, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystal structure of a protein acetyltransferase, HP0935
Authors: Dadireddy, V. / Mahanta, P. / Kumar, A. / Desirazu, R.N. / Ramakumar, S.
History
DepositionApr 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conf
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _entity.pdbx_fragment / _entity.pdbx_number_of_molecules / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.pdbx_netI_over_av_sigmaI / _reflns.pdbx_number_measured_all / _software.classification / _software.name / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Description: Real space R-factor
Details: Earlier structure was refined with twin refinement ON, using REFMAC5. The current model was refined with twin refinement OFF.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein
C: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,70618
Polymers55,8803
Non-polymers82615
Water5,080282
1
A: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8836
Polymers18,6271
Non-polymers2565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9797
Polymers18,6271
Non-polymers3526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8445
Polymers18,6271
Non-polymers2174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.856, 66.170, 70.904
Angle α, β, γ (deg.)90.000, 91.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-201-

K

21C-384-

HOH

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Components

#1: Protein N-acetyltransferase domain-containing protein


Mass: 18626.504 Da / Num. of mol.: 3 / Fragment: GNAT-domain / Mutation: M1V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_0935 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): star / References: UniProt: O25589
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.47 Å3/Da / Density % sol: 50.26 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M potassium thiocyanate, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) polyethylene glycol 3500, 20% (w/v) ethylene glycol (cryo, soaked)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.9
111/2H-3/2K, -1/2H-1/2K, -L20.1
ReflectionResolution: 2→70.88 Å / Num. obs: 36953 / % possible obs: 99.8 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.045 / Rrim(I) all: 0.129 / Net I/σ(I): 10.4 / Num. measured all: 273069
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.055.20.5861420327240.7920.2830.6522.5100
8.94-70.889.10.05840224420.9970.020.06224.198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.27 Å58.91 Å
Translation3.27 Å58.91 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimless0.7.9data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.28data extraction
PROTEUM PLUSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→70.88 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.068 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1880 5.1 %RANDOM
Rwork0.2152 ---
obs0.2169 35062 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.32 Å2 / Biso mean: 21.815 Å2 / Biso min: 7.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.22 Å2
2--0.41 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 2→70.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 42 282 3927
Biso mean--31.32 28.53 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123738
X-RAY DIFFRACTIONr_bond_other_d0.0040.0163525
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.6455015
X-RAY DIFFRACTIONr_angle_other_deg0.6991.5658146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9765461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.099510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42210650
X-RAY DIFFRACTIONr_chiral_restr0.0990.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024222
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02838
X-RAY DIFFRACTIONr_mcbond_it1.621.2521853
X-RAY DIFFRACTIONr_mcbond_other1.5891.2491851
X-RAY DIFFRACTIONr_mcangle_it2.2532.2212296
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 116 -
Rwork0.241 2607 -
all-2723 -
obs--100 %
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)
11.8638-0.94870.04961.8386-0.10742.4194-0.04250.1662-0.0035-0.15640.0074-0.0696-0.1137-0.18080.03510.0319-0.01270.01010.0615-0.01770.00820.716-10.691-87.17
21.07230.47210.31133.25140.32842.1084-0.00620.15330.0157-0.1310.00480.0720.25850.09980.00150.05170.02010.00740.03530.01180.0135-14.903-8.448-87.131
32.87390.7916-0.18280.6460.10812.3870.01640.1739-0.0104-0.1547-0.008-0.0612-0.1760.2208-0.00840.07150.00760.00980.04510.01050.02870.786-40.153-87.376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 161
2X-RAY DIFFRACTION1A201 - 205
3X-RAY DIFFRACTION2B0 - 161
4X-RAY DIFFRACTION2B201 - 206
5X-RAY DIFFRACTION3C-1 - 160
6X-RAY DIFFRACTION3C201 - 204

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