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- PDB-3mqh: crystal structure of the 3-N-acetyl transferase WlbB from Bordete... -

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Basic information

Entry
Database: PDB / ID: 3mqh
Titlecrystal structure of the 3-N-acetyl transferase WlbB from Bordetella petrii in complex with CoA and UDP-3-amino-2-acetamido-2,3-dideoxy glucuronic acid
ComponentsLipopolysaccharides biosynthesis acetyltransferase
KeywordsTRANSFERASE / beta helix / acetyltransferase
Function / homology
Function and homology information


acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / nucleotide binding
Similarity search - Function
Ubiquitin Ligase Nedd4; Chain: W; - #110 / : / Ubiquitin Ligase Nedd4; Chain: W; / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Single Sheet / Mainly Beta
Similarity search - Domain/homology
COENZYME A / Chem-MJZ / PHOSPHATE ION / Lipopolysaccharides biosynthesis acetyltransferase
Similarity search - Component
Biological speciesBordetella petrii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.43 Å
Authorsthoden, J.B. / holden, H.M.
CitationJournal: Biochemistry / Year: 2010
Title: Molecular structure of WlbB, a bacterial N-acetyltransferase involved in the biosynthesis of 2,3-diacetamido-2,3-dideoxy-D-mannuronic acid .
Authors: Thoden, J.B. / Holden, H.M.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Lipopolysaccharides biosynthesis acetyltransferase
B: Lipopolysaccharides biosynthesis acetyltransferase
C: Lipopolysaccharides biosynthesis acetyltransferase
D: Lipopolysaccharides biosynthesis acetyltransferase
E: Lipopolysaccharides biosynthesis acetyltransferase
F: Lipopolysaccharides biosynthesis acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,29235
Polymers124,6306
Non-polymers9,66229
Water30,5891698
1
A: Lipopolysaccharides biosynthesis acetyltransferase
B: Lipopolysaccharides biosynthesis acetyltransferase
C: Lipopolysaccharides biosynthesis acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,38519
Polymers62,3153
Non-polymers5,07116
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14130 Å2
ΔGint2 kcal/mol
Surface area20410 Å2
MethodPISA
2
D: Lipopolysaccharides biosynthesis acetyltransferase
E: Lipopolysaccharides biosynthesis acetyltransferase
F: Lipopolysaccharides biosynthesis acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,90716
Polymers62,3153
Non-polymers4,59213
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-10 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.466, 107.891, 91.269
Angle α, β, γ (deg.)90.00, 102.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Lipopolysaccharides biosynthesis acetyltransferase


Mass: 20771.611 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella petrii (bacteria) / Strain: ATCC BAA-461, DSM 12804, CCUG 43448 / Gene: Bpet4817, wlbB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: A9IH93, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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Non-polymers , 7 types, 1727 molecules

#2: Chemical
ChemComp-MJZ / (2S,3S,4R,5R,6R)-5-(acetylamino)-4-amino-6-{[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3-hydroxytetrahydro-2H-pyran-2-carboxylic acid


Mass: 620.352 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H26N4O17P2
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1698 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16-20% PEG3400, 210 mM tetramethylammonium chloride, 100 mM HEPPS, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 14, 2009
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. all: 213775 / Num. obs: 213775 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 28.3
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 6.6 / Num. unique all: 17966 / Rsym value: 0.125 / % possible all: 76.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0066refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3MQG

3mqg


Resolution: 1.43→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 0.902 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20645 10686 5 %RANDOM
Rwork0.17417 ---
all0.176 213775 --
obs0.17578 203089 89.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.52 Å2
2---0.74 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.43→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8690 0 612 1698 11000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0219609
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1241.99913138
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.54751174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89422.767430
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.373151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4361594
X-RAY DIFFRACTIONr_chiral_restr0.1450.21457
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217276
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2911.55687
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97529152
X-RAY DIFFRACTIONr_scbond_it3.22233922
X-RAY DIFFRACTIONr_scangle_it4.9894.53969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 667 -
Rwork0.235 12154 -
obs--73.36 %

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