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- PDB-7s3u: Crystal structure of an N-acetyltransferase from Helicobacter pul... -

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Basic information

Entry
Database: PDB / ID: 7s3u
TitleCrystal structure of an N-acetyltransferase from Helicobacter pullorum in the presence of Coenzyme A and dTDP-3-amino-3,6-dideoxy-D-glucose
ComponentsN-acetyltransferase
KeywordsTRANSFERASE
Function / homologyCOENZYME A / Chem-T3Q
Function and homology information
Biological speciesHelicobacter pullorum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 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)19,5324
Polymers18,1551
Non-polymers1,3773
Water3,171176
1
A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules

A: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,59512
Polymers54,4643
Non-polymers4,1319
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area12040 Å2
ΔGint-11 kcal/mol
Surface area15290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.970, 102.970, 102.970
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-473-

HOH

21A-476-

HOH

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Components

#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)
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-T3Q / [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate / thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose


Mass: 547.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N3O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16-20% PEG-3350, 200 mM KCl, 5 mM dTDP-3-amino-3,6-dideoxy-D-glucose, 5 mM Coenzyme A, 100 mM HEPPS

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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: Aug 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 32307 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Rsym value: 0.044 / Net I/σ(I): 18.7
Reflection shellResolution: 1.456→1.55 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 5.1 / Num. unique obs: 5844 / Rsym value: 0.214 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4mzu

4mzu


Resolution: 1.45→36.43 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.155 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 1553 4.8 %RANDOM
Rwork0.1717 ---
obs0.1726 30754 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.85 Å2 / Biso mean: 11.482 Å2 / Biso min: 4.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.45→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 87 176 1370
Biso mean--12.55 25.01 -
Num. residues----145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131247
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171143
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.6521709
X-RAY DIFFRACTIONr_angle_other_deg1.3541.5772675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.11224.4949
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97215203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.348152
X-RAY DIFFRACTIONr_chiral_restr0.0790.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
LS refinement shellResolution: 1.45→1.486 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.352 88 -
Rwork0.336 2285 -
obs--98.18 %

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