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- PDB-8iyo: Crystal structure of a protein acetyltransferase, HP0935, acetyl-... -

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Basic information

Entry
Database: PDB / ID: 8iyo
TitleCrystal structure of a protein acetyltransferase, HP0935, acetyl-CoA bound form
ComponentsN-acetyltransferase domain-containing protein
KeywordsTRANSFERASE / GNAT domain / protein acetyltransferase / acetyl-coenzyme A
Function / homology: / protein-N-terminal-alanine acetyltransferase activity / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / N-acetyltransferase domain-containing protein
Function and homology information
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsDadireddy, V. / Mahanta, P. / Kumar, A. / Desirazu, R.N. / Ramakumar, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Biochemical and structural characterization of a GNAT superfamily protein acetyltransferase from Helicobacter pylori.
Authors: Dadireddy, V. / Kumar, A. / Kumar, S. / Sarma, S.P. / Mahanta, P. / Ramakumar, S. / Desirazu, R.N.
History
DepositionApr 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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
D: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7448
Polymers74,5064
Non-polymers3,2384
Water1,35175
1
A: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4362
Polymers18,6271
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-2 kcal/mol
Surface area8730 Å2
MethodPISA
2
B: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4362
Polymers18,6271
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-2 kcal/mol
Surface area8830 Å2
MethodPISA
3
C: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4362
Polymers18,6271
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-2 kcal/mol
Surface area8760 Å2
MethodPISA
4
D: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4362
Polymers18,6271
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-2 kcal/mol
Surface area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.797, 87.797, 216.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
N-acetyltransferase domain-containing protein


Mass: 18626.504 Da / Num. of mol.: 4 / 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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.23 Å3/Da / Density % sol: 61.93 % / Description: Needles
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02M magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 22% (w/v) poly(acrylic acid, sodium salt) 5100, ethylene glycol (cryo, soaked)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.4→44.08 Å / Num. obs: 36841 / % possible obs: 100 % / Redundancy: 18.3 % / Biso Wilson estimate: 46.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.036 / Rrim(I) all: 0.154 / Net I/σ(I): 15.2 / Num. measured all: 675020 / Scaling rejects: 3
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
2.4-2.49191.4187346038730.9010.3321.4572.799.9
8.98-44.0817.40.0531258672410.0130.05443.499

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.51 Å44.07 Å
Translation3.51 Å44.07 Å

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Processing

Software
NameVersionClassification
Aimless0.7.9data scaling
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.08 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 1889 5.15 %
Rwork0.1758 34822 -
obs0.1777 36711 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.77 Å2 / Biso mean: 58.7408 Å2 / Biso min: 33.12 Å2
Refinement stepCycle: final / Resolution: 2.4→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 204 75 5431
Biso mean--58.31 50.36 -
Num. residues----649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.460.31241480.254826762824
2.47-2.540.30011410.238726842825
2.54-2.620.27571400.230526582798
2.62-2.710.26121690.24126642833
2.71-2.820.28821370.228326832820
2.82-2.950.27921410.215226632804
2.95-3.110.25831450.215526892834
3.11-3.30.22261410.209526722813
3.3-3.550.21851600.194326562816
3.55-3.910.22681390.165926882827
3.91-4.480.17381490.142626892838
4.48-5.640.16991470.134426842831
5.64-44.080.17131320.142627162848
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)
13.98320.17381.36792.16780.61663.0528-0.05760.06090.11130.0805-0.0405-0.0203-0.1458-0.02090.09310.25120.0006-0.01760.33650.01310.362246.168.486-2.153
22.8341-0.66753.4682.4116-1.41628.9551-0.2241-0.27880.06160.14820.24620.009-0.8875-0.2775-0.0320.58660.05140.00260.49910.06530.438330.9415.886-38.077
31.9950.25960.91812.5805-1.71294.60520.0992-0.0726-0.0695-0.012-0.05620.06860.2462-0.1239-0.03640.28890.050.02280.30750.02140.389772.6266.913-28.2
42.86350.4507-0.17273.34860.5555.23050.00280.12590.0940.17510.00280.06250.3583-0.2720.00190.2647-0.005-0.03020.35670.00180.361516.715-6.772-12.455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:161 OR RESID 201:201 ) )A0 - 161
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 0:161 OR RESID 201:201 ) )A201
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID -1:160 OR RESID 201:201 ) )B-1 - 160
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID -1:160 OR RESID 201:201 ) )B201
5X-RAY DIFFRACTION3( CHAIN C AND ( RESID -1:160 OR RESID 201:201 ) )C-1 - 160
6X-RAY DIFFRACTION3( CHAIN C AND ( RESID -1:160 OR RESID 201:201 ) )C201
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID -1:161 OR RESID 201:201 ) )D-1 - 161
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID -1:161 OR RESID 201:201 ) )D201

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