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- PDB-4xpl: The crystal structure of Campylobacter jejuni N-acetyltransferase... -

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Basic information

Entry
Database: PDB / ID: 4xpl
TitleThe crystal structure of Campylobacter jejuni N-acetyltransferase PseH in complex with acetyl coenzyme A
ComponentsN-Acetyltransferase, PseH
KeywordsTRANSFERASE / Campylobacter jejuni / PseH / bacterial glycosylation / N-acetyltransferase
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / N-Acetyltransferase, PseH / :
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni PT14 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSong, W.S. / Nam, M.S. / Namgung, B. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Structural analysis of PseH, the Campylobacter jejuni N-acetyltransferase involved in bacterial O-linked glycosylation.
Authors: Song, W.S. / Nam, M.S. / Namgung, B. / Yoon, S.I.
History
DepositionJan 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-Acetyltransferase, PseH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1892
Polymers19,3791
Non-polymers8101
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.421, 110.495, 40.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein N-Acetyltransferase, PseH


Mass: 19379.373 Da / Num. of mol.: 1
Mutation: M1L, N107S, D120S, R122H, H144Y, I145V, C146Y, D151N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni PT14 (Campylobacter)
Gene: A911_06385 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K0HK73, UniProt: A0A0J9X276*PLUS
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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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: 50.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 28% PEG 300, 10mM beta-mercaptoethanol, 0.1M phosphate-citrate, 10mM acetyl coenzyme A
PH range: 4.4 / Temp details: incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen cryo-stream
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 14434 / % possible obs: 98.2 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.078 / Χ2: 2.139 / Net I/av σ(I): 35.1 / Net I/σ(I): 12.5 / Num. measured all: 87513
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.026.20.46314211.58498.5
2.02-2.16.20.3313971.76998
2.1-2.26.10.27614111.83898.1
2.2-2.316.10.2114081.93998.3
2.31-2.4660.17214241.96697.2
2.46-2.655.90.13414172.11797.7
2.65-2.915.90.09714142.32596.3
2.91-3.335.80.07314392.62698.1
3.33-4.26.20.05315072.71899.8
4.2-306.20.04715962.44999.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XPK

4xpk


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 713 5 %RANDOM
Rwork0.1878 13563 --
obs0.1898 13563 97.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.64 Å2 / Biso mean: 29.9 Å2 / Biso min: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--2.1 Å20 Å2
3----1.94 Å2
Refinement stepCycle: final / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1182 0 51 77 1310
Biso mean--43.91 35.41 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221262
X-RAY DIFFRACTIONr_bond_other_d00.02847
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9991704
X-RAY DIFFRACTIONr_angle_other_deg4.02332073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.93225.08559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93515229
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.85151
X-RAY DIFFRACTIONr_chiral_restr0.0890.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021332
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02265
X-RAY DIFFRACTIONr_mcbond_it0.7631.5703
X-RAY DIFFRACTIONr_mcbond_other01.5284
X-RAY DIFFRACTIONr_mcangle_it1.43821133
X-RAY DIFFRACTIONr_scbond_it2.2293559
X-RAY DIFFRACTIONr_scangle_it3.6624.5571
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rfree0.315 58 -
Rwork0.246 974 -
obs--98.1 %
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)
11.72861.088-4.25321.1088-1.576113.5050.21530.01890.11560.25440.07940.0468-0.2319-0.0799-0.29470.27110.0271-0.03010.2177-0.0070.247718.7822.35133.276
23.4306-1.4220.05693.14230.66762.21360.0118-0.0085-0.01460.00360.0472-0.03910.01630.0228-0.0590.1123-0.0049-0.00240.02130.00380.179417.15719.38418.539
35.6526-0.0332-0.79318.7591-0.86912.95260.0199-0.0659-0.2353-0.0304-0.03050.59630.2255-0.14760.01050.1974-0.0272-0.03750.0593-0.03290.287511.0966.20214.202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 52
2X-RAY DIFFRACTION2A53 - 111
3X-RAY DIFFRACTION3A112 - 154

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