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- PDB-2vhe: PglD-CoA complex: An acetyl transferase from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 2vhe
TitlePglD-CoA complex: An acetyl transferase from Campylobacter jejuni
ComponentsACETYLTRANSFERASE
KeywordsTRANSFERASE / COENZYME A / N-ACETYL TRANSFERASE
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
COENZYME A / UDP-N-acetylbacillosamine N-acetyltransferase
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRangarajan, E.S. / Ruane, K.M. / Sulea, T. / Watson, D.C. / Proteau, A. / Leclerc, S. / Cygler, M. / Matte, A. / Young, N.M.
CitationJournal: 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.
History
DepositionNov 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 28, 2011Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.3Nov 2, 2022Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Jan 31, 2024Group: 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: ACETYLTRANSFERASE
B: ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8146
Polymers42,0872
Non-polymers1,7274
Water4,738263
1
A: ACETYLTRANSFERASE
hetero molecules

A: ACETYLTRANSFERASE
hetero molecules

A: ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,01012
Polymers63,1313
Non-polymers2,8799
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6120 Å2
ΔGint-56.6 kcal/mol
Surface area27980 Å2
MethodPQS
2
B: ACETYLTRANSFERASE
hetero molecules

B: ACETYLTRANSFERASE
hetero molecules

B: ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4336
Polymers63,1313
Non-polymers2,3033
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6500 Å2
ΔGint-50.3 kcal/mol
Surface area25110 Å2
MethodPQS
Unit cell
Length a, b, c (Å)99.250, 99.250, 143.027
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

21B-511-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9907, -0.1361, -0.008404), (0.1361, 0.9907, -0.006127), (0.00916, 0.004926, 0.9999)
Vector: 0.4016, 0.6243, -71.73)

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Components

#1: Protein ACETYLTRANSFERASE / N-ACETYLTRANSFERASE


Mass: 21043.553 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(RIPL)
References: UniProt: Q0P9D1, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST XXX CORESPOND TO THE TAG. NO. STARTS FROM ALA 2. EXPAND

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.92 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM CITRATE PH 5.6, 0.16 M SODIUM TARTRATE AND 2.0 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 48692 / % possible obs: 100 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NPO

2npo


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.977 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 36-46 AND 182-183 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2457 5.1 %RANDOM
Rwork0.19 ---
obs0.191 46151 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 106 263 3179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222999
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6042.0084058
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4245379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.85225.596109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33515531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.317156
X-RAY DIFFRACTIONr_chiral_restr0.1060.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022124
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.21421
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22043
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.2102
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.881.51922
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34122988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28931208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4174.51066
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 184
Rwork0.273 3388
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)
11.86890.4277-0.65790.7314-0.17870.73070.0148-0.01210.11340.0436-0.0141-0.1242-0.05120.0726-0.0007-0.0543-0.02430.0085-0.0561-0.0197-0.002614.74110.076-0.138
21.5870.3436-0.41750.8383-0.16961.0379-0.13520.19360.1058-0.1519-0.0203-0.1639-0.04830.10270.1555-0.0319-0.02880.0225-0.02230.06970.012114.8928.16671.543
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 195
2X-RAY DIFFRACTION2B2 - 195

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