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- PDB-7s41: Crystal structure of an N-acetyltransferase from Helicobacter pul... -

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Basic information

Entry
Database: PDB / ID: 7s41
TitleCrystal structure of an N-acetyltransferase from Helicobacter pullorum in the presence of Coenzyme A and dTDP-3-acetamido-3,6-dideoxy-D-glucose
ComponentsN-acetyltransferase
KeywordsTRANSFERASE
Function / homologyChem-87N / COENZYME A
Function and homology information
Biological speciesHelicobacter pullorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 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)NIH 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)19,7838
Polymers18,1551
Non-polymers1,6287
Water3,423190
1
A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,34924
Polymers54,4643
Non-polymers4,88521
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area13600 Å2
ΔGint-9 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.965, 102.965, 102.965
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-207-

NA

21A-475-

HOH

31A-488-

HOH

41A-490-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-acetyltransferase


Mass: 18154.758 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, 197 molecules

#2: Chemical ChemComp-87N / [(2~{R},3~{R},4~{S},5~{S},6~{R})-4-acetamido-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 589.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H29N3O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG-5000, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM coenzyme A, 100 mM HEPES. Crystals were harvested and soaked in 20% PEG-5000, 200 mM NaCl, 5 mM dTDP-3-amino-3,6-dideoxy-D- ...Details: 15% PEG-5000, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM coenzyme A, 100 mM HEPES. Crystals were harvested and soaked in 20% PEG-5000, 200 mM NaCl, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM acetyl coenzyme A, 100 mM HEPES

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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: Sep 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 35803 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.1 % / Rsym value: 0.041 / Net I/σ(I): 4.5
Reflection shellResolution: 1.5→1.5 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 4.5 / Num. unique obs: 6639 / Rsym value: 0.234 / % possible all: 99.9

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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: 1.4→36.43 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.99 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1826 1755 4.9 %RANDOM
Rwork0.1628 ---
obs0.1638 34048 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.79 Å2 / Biso mean: 12.433 Å2 / Biso min: 4.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.4→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 55 190 1400
Biso mean--16.39 27.62 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171170
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.751738
X-RAY DIFFRACTIONr_angle_other_deg1.3761.6452740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0625156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.88925.10647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74415204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.917152
X-RAY DIFFRACTIONr_chiral_restr0.380.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021357
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02227
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 129 -
Rwork0.313 2484 -
all-2613 -
obs--99.85 %

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