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- PDB-3bsw: PglD-citrate complex, from Campylobacter jejuni NCTC 11168 -

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Basic information

Entry
Database: PDB / ID: 3bsw
TitlePglD-citrate complex, from Campylobacter jejuni NCTC 11168
ComponentsAcetyltransferase
KeywordsTRANSFERASE / left-hand beta helix / hexapeptide repeat / UDP / acetyl coenzyme Z / Rossmann fold / bacillosamine / campylobacter / pgl / N-linked glycosylation
Function / homology
Function and homology information


UDP-N-acetylbacillosamine N-acetyltransferase / protein N-linked glycosylation via asparagine / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid ...Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / UDP-N-acetylbacillosamine N-acetyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.77 Å
Model detailsPglD with native substrate from Campylobacter jejuni, NCTC 11168
AuthorsOlivier, N.B. / Imperiali, B.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal structure and catalytic mechanism of PglD from Campylobacter jejuni.
Authors: Olivier, N.B. / Imperiali, B.
History
DepositionDec 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5822
Polymers21,3901
Non-polymers1921
Water3,711206
1
A: Acetyltransferase
hetero molecules

A: Acetyltransferase
hetero molecules

A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7466
Polymers64,1703
Non-polymers5763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area6320 Å2
ΔGint-43 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.347, 86.347, 65.538
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

21A-277-

HOH

31A-292-

HOH

41A-305-

HOH

51A-313-

HOH

Detailsbiological unit is a trimer generated from the monomer asymmetric unit by the operations -x+y,-x,z and -y,x-y,z

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Components

#1: Protein Acetyltransferase


Mass: 21389.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal residues GSA are non-native; resulted from removal of N-terminal His-tag by thrombin
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: NCTC 11168 / Gene: pglD / Plasmid: pETGQ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0P9D1, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.362.7
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop8SeMet derivative: 1 M sodium citrate, 100 mM imidazole, pH 8.0 in the resevior; protein solution containing 20 mM HEPES, 150 mM NaCl, pH 7.1, protein concentration of 10 mg/mL; drop made by mixing 1.5 uL of protein and resevoir solutions, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop4.2Native: 20% PEG 1000, 100 mM phosphate-citrate, 200 mM Li2SO4, pH 4.2 in the resevior; protein solution containing 20 mM HEPES, 150 mM NaCl, pH 7.1, protein concentration of 10 mg/mL; drop made by mixing 1.5 uL of protein and resevoir solutions, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9784 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2007 / Details: Toroidal focusing mirror
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 5 / Number: 80527 / Rmerge(I) obs: 0.136 / Χ2: 1.01 / D res high: 2.2 Å / D res low: 30 Å / Num. obs: 14285 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.733099.910.0561.6545.4
3.764.7310010.0521.1535.6
3.293.7610010.0961.1085.6
2.993.2910010.1420.8875.7
2.772.9910010.2030.8695.7
2.612.7710010.350.9175.7
2.482.6110010.4070.9195.7
2.372.4810010.4770.8215.6
2.282.3710010.4780.855.7
2.22.2810010.6180.9235.6
ReflectionResolution: 1.77→30 Å / Num. all: 27293 / Num. obs: 27129 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 25.11 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.7
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2695 / % possible all: 99.6

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.77→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.095 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Heavy atom sites in the substructure were identified using SHELX-D with data collected at the Se peak wavelength and truncated to 2.5 . Three out of five possible selenium sites for a single ...Details: Heavy atom sites in the substructure were identified using SHELX-D with data collected at the Se peak wavelength and truncated to 2.5 . Three out of five possible selenium sites for a single molecule of PglD in the asymmetric were located; CC All/weak=17.15/11.12, PATFOM 18.32. Structure factors from the native data were merged with initial phases using CAD (Riso=12%); phase extension to 1.77 and density modification were carried out using SHELX-E; values for contrast, connectivity, mean mapCC, and pseudo-free CC were 1.07, 0.96, 0.94, and 80.09%, respectively. The initial model was built with ARP/wARP (Perrakis et al., 2001) using the automated tracing function and manual adjustments were made using COOT (Emsley and Cowtan, 2004) and O (Jones et al., 1991).
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1360 5 %RANDOM
Rwork0.183 ---
obs0.184 27106 99.71 %-
all-27185 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.892 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.77→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 13 206 1616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221432
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9651940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8125.10249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27815235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.401153
X-RAY DIFFRACTIONr_chiral_restr0.0830.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021051
X-RAY DIFFRACTIONr_nbd_refined0.2080.2746
X-RAY DIFFRACTIONr_nbtor_refined0.310.21000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.224
X-RAY DIFFRACTIONr_mcbond_it0.6971.5944
X-RAY DIFFRACTIONr_mcangle_it1.29121504
X-RAY DIFFRACTIONr_scbond_it2.1383488
X-RAY DIFFRACTIONr_scangle_it3.4974.5434
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 101 -
Rwork0.247 1901 -
all-2002 -
obs-2020 99.55 %

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