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- PDB-3bfp: Crystal Structure of apo-PglD from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 3bfp
TitleCrystal Structure of apo-PglD from Campylobacter jejuni
ComponentsAcetyltransferase
KeywordsTRANSFERASE / left-handed beta helix / N-acetyltransferase / CoA binding protein / N-glycan biosynthesis / bacillosamine / Structural Genomics / MKBSGI / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
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 / Rossmann fold ...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
CITRATE ANION / UDP-N-acetylbacillosamine N-acetyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsRangarajan, E.S. / Watson, D.C. / Leclerc, S. / Proteau, A. / Cygler, M. / Matte, A. / Young, N.M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
Citation
Journal: Biochemistry / Year: 2008
Title: Structure and Active Site Residues of PglD, an N-Acetyltransferase from the Bacillosamine Synthetic Pathway Required for N-Glycan Synthesis in Campylobacter jejuni.
Authors: Rangarajan, E.S. / Ruane, K.M. / Sulea, T. / Watson, D.C. / Proteau, A. / Leclerc, S. / Cygler, M. / Matte, A. / Young, N.M.
#1: Journal: Biochemistry / Year: 2006
Title: In vitro biosynthesis of UDP-N,N'-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system
Authors: Olivier, N.B. / Chen, M.M. / Behr, J.R. / Imperiali, B.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Structure of the N-linked glycan present in multiple glycoproteins in the gram-negative bacterium Campylobacter jejuni
Authors: Young, N.M. / Brisson, J.R. / Kelly, J. / Watson, D.C. / Tessier, L. / Lanthier, P.H. / Cadotte, N. / Michael, F.St. / Aberg, E. / Szymanski, C.M.
#3: Journal: Structure / Year: 2006
Title: Conformational and sequence signatures in beta-helix proteins
Authors: Lengar, P. / Joshi, N.V. / Balaram, P.
History
DepositionNov 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)21,2332
Polymers21,0441
Non-polymers1891
Water2,090116
1
A: Acetyltransferase
hetero molecules

A: Acetyltransferase
hetero molecules

A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6986
Polymers63,1313
Non-polymers5673
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.462, 86.462, 65.547
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-196-

HOH

21A-207-

HOH

31A-283-

HOH

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Components

#1: Protein Acetyltransferase /


Mass: 21043.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: pglD / Plasmid: pCWori+ / Production host: Escherichia coli (E. coli) / Strain (production host): AD202 / References: UniProt: Q0P9D1
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-tris pH 6.5, 0.15 M ammonium acetate, 26% (v/v) PEG400 or 0.1 M Bis-tris pH 6.5, 0.2M postassium acetate, 21% (v/v) PEG 400, vapor diffusion, sitting drop, temperature 20K, VAPOR ...Details: 0.1 M Bis-tris pH 6.5, 0.15 M ammonium acetate, 26% (v/v) PEG400 or 0.1 M Bis-tris pH 6.5, 0.2M postassium acetate, 21% (v/v) PEG 400, vapor diffusion, sitting drop, temperature 20K, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU FR-D11.5418
SYNCHROTRONNSLS X8C21.1
Detector
TypeIDDetector
MAR scanner 345 mm plate1IMAGE PLATE
ADSC QUANTUM 42CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1MIRRORS
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.11
ReflectionResolution: 1.75→50 Å / Num. obs: 28194 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rsym value: 0.048 / Net I/σ(I): 19.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3 / Num. unique all: 2779 / Rsym value: 0.488 / % possible all: 99

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 1.75→32.51 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.928 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1420 5.1 %RANDOM
Rwork0.198 ---
obs0.2 28118 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.584 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→32.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1423 0 13 116 1552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221462
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9751982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1425.93259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65815264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.005153
X-RAY DIFFRACTIONr_chiral_restr0.0840.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021082
X-RAY DIFFRACTIONr_nbd_refined0.1990.2700
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.220
X-RAY DIFFRACTIONr_mcbond_it0.8171.5956
X-RAY DIFFRACTIONr_mcangle_it1.40521503
X-RAY DIFFRACTIONr_scbond_it2.3243560
X-RAY DIFFRACTIONr_scangle_it3.7044.5472
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 120 -
Rwork0.287 1931 -
all-2051 -
obs--98.84 %

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