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- PDB-7s45: Crystal structure of an N-acetyltransferase, C80T mutant, from He... -

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Basic information

Entry
Database: PDB / ID: 7s45
TitleCrystal structure of an N-acetyltransferase, C80T mutant, from Helicobacter pullorum in the presence of Acetyl Coenzyme A and dTDP
ComponentsN-acetyltransferase
KeywordsTRANSFERASE
Function / homologyACETYL COENZYME *A / THYMIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesHelicobacter pullorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGriffiths, W.A. / Spencer, K.D. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Biochemical investigation of an N-acetyltransferase from Helicobacter pullorum.
Authors: Griffiths, W.A. / Spencer, K.D. / Thoden, J.B. / Holden, H.M.
History
DepositionSep 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
A: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7607
Polymers18,1531
Non-polymers1,6076
Water3,657203
1
A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,28021
Polymers54,4583
Non-polymers4,82218
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Buried area15540 Å2
ΔGint-11 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.452, 103.452, 103.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-463-

HOH

31A-487-

HOH

41A-500-

HOH

51A-503-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-acetyltransferase /


Mass: 18152.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pullorum (bacteria) / Strain: NAP8W25 / Gene: BA919_rs02330 / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS


Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG-8000, 2% MPD, 5 mM dTDP, 5 mM acetyl coenzyme A, 100 mM MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Apr 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 57433 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rsym value: 0.047 / Net I/σ(I): 13.7
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 12226 / Rsym value: 0.247 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7s3u

7s3u


Resolution: 1.2→32.74 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 0.576 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 2805 4.9 %RANDOM
Rwork0.1743 ---
obs0.175 54628 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.35 Å2 / Biso mean: 10.013 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.2→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 126 203 1400
Biso mean--13.55 23.74 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131276
X-RAY DIFFRACTIONr_bond_other_d00.0171198
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.7011752
X-RAY DIFFRACTIONr_angle_other_deg1.3171.612803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4675157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.27325.21746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41215210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.705152
X-RAY DIFFRACTIONr_chiral_restr0.3930.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021334
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02225
LS refinement shellResolution: 1.2→1.23 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.269 200 -
Rwork0.276 3999 -
obs--99.69 %

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