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- PDB-4xpk: The crystal structure of Campylobacter jejuni N-acetyltransferase PseH -

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Basic information

Entry
Database: PDB / ID: 4xpk
TitleThe crystal structure of Campylobacter jejuni N-acetyltransferase PseH
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
N-Acetyltransferase, PseH / :
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni PT14 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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


Theoretical massNumber of molelcules
Total (without water)19,3791
Polymers19,3791
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.558, 111.033, 41.045
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 22-24% PEG MME 550, 4mM reduced glutathione, 4mM oxidized glutathione, 0.1M phosphate-citrate
PH range: 4.4-4.6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen cryo-stream
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 14574 / % possible obs: 98.3 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Χ2: 3.104 / Net I/av σ(I): 43 / Net I/σ(I): 23.2 / Num. measured all: 79770
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.025.60.42114270.9040.1910.4642.05799.5
2.02-2.15.60.29814340.9360.1350.3282.31999.3
2.1-2.25.60.2314530.9660.1040.2532.51199.1
2.2-2.315.70.17814330.9780.080.1962.71498.8
2.31-2.465.60.14114450.9880.0640.1562.92198.7
2.46-2.655.60.10714420.9910.0490.1183.1298
2.65-2.915.50.0814240.9940.0370.0893.64896.5
2.91-3.335.30.06314280.9950.030.074.19896.2
3.33-4.25.20.04915060.9970.0240.0554.20599.1
4.2-305.10.04115820.9990.0190.0453.52197.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4jjx


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 736 5.1 %RANDOM
Rwork0.1971 13737 --
obs0.1989 13737 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 72.01 Å2 / Biso mean: 32.9 Å2 / Biso min: 14.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--1.46 Å20 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 0 40 1215
Biso mean---36.57 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221202
X-RAY DIFFRACTIONr_bond_other_d00.02821
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9521616
X-RAY DIFFRACTIONr_angle_other_deg4.09332013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3125139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.61925.43957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88815227
X-RAY DIFFRACTIONr_chiral_restr0.1010.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021290
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02249
X-RAY DIFFRACTIONr_mcbond_it0.921.5701
X-RAY DIFFRACTIONr_mcbond_other01.5286
X-RAY DIFFRACTIONr_mcangle_it1.79221132
X-RAY DIFFRACTIONr_scbond_it2.9113501
X-RAY DIFFRACTIONr_scangle_it4.7774.5484
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rfree0.274 52 -
Rwork0.209 968 -
obs--95.68 %
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)
11.51790.9999-2.65840.7435-1.118910.5310.1656-0.020.10650.15670.02640.0848-0.323-0.0536-0.1920.28090.055-0.00630.2890.00410.19618.27822.55232.842
23.0364-1.6717-0.05113.90220.56842.19020.0011-0.0096-0.05520.03420.0619-0.0051-0.01210.0027-0.0630.0145-0.004-0.00010.07360.00150.086416.84919.32118.532
36.6173-1.32640.058310.428-1.71984.2936-0.0664-0.2645-0.37730.2050.08671.10050.1565-0.3054-0.02020.0883-0.02320.02130.1217-0.02230.238411.1116.05914.236
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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