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- PDB-3nu7: WbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in... -

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Basic information

Entry
Database: PDB / ID: 3nu7
TitleWbpE, an Aminotransferase from Pseudomonas aeruginosa Involved in O-antigen Assembly in Complex with the Cofactor PMP
ComponentsAminotransferase WbpE
KeywordsTRANSFERASE / Domain-swapped beta hairpin / Aminotransferase / PLP / PMP / UDP-GlcNAc(3NH2)A / Lipopolysaccharide / O-antigen / B-band
Function / homology
Function and homology information


UDP-2-acetamido-2-deoxy-ribo-hexuluronate aminotransferase / UDP-glucuronate biosynthetic process / O antigen biosynthetic process / polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / transaminase activity / cell wall organization / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLarkin, A. / Olivier, N.B. / Imperiali, B.
CitationJournal: Biochemistry / Year: 2010
Title: Structural Analysis of WbpE from Pseudomonas aeruginosa PAO1: A Nucleotide Sugar Aminotransferase Involved in O-Antigen Assembly
Authors: Larkin, A. / Olivier, N.B. / Imperiali, B.
History
DepositionJul 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase WbpE
B: Aminotransferase WbpE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7047
Polymers77,9312
Non-polymers7735
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-26 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.280, 149.288, 54.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Aminotransferase WbpE


Mass: 38965.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1-LAC / Gene: PA3155, wbpE / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9HZ76
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Crystallization conditions: 0.1 M Bis-Tris, pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350 in the reservoir; Protein solution contains 25 mM HEPES, pH 8.0, 100 mM NaCl, 0.5% glycerol; Drop ...Details: Crystallization conditions: 0.1 M Bis-Tris, pH 5.5, 0.2 M Ammonium sulfate, 25% PEG 3350 in the reservoir; Protein solution contains 25 mM HEPES, pH 8.0, 100 mM NaCl, 0.5% glycerol; Drop made by mixing 1.5 uL of protein and reservoir solutions., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2009 / Details: Toroidal Focusing Mirror
RadiationMonochromator: SI(111) Channel Cut Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 45308 / % possible obs: 99.8 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 53.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 14.5 % / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet Derivative

Resolution: 1.95→34.66 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.117 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 2417 5.1 %RANDOM
Rwork0.19915 ---
obs0.20152 45308 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.367 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→34.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5423 0 50 377 5850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225576
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9817594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5945717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60324.632231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54615896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6761531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2884
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214217
X-RAY DIFFRACTIONr_mcbond_it0.5351.53580
X-RAY DIFFRACTIONr_mcangle_it0.96225777
X-RAY DIFFRACTIONr_scbond_it1.50131996
X-RAY DIFFRACTIONr_scangle_it2.5294.51816
LS refinement shellResolution: 1.949→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 162 -
Rwork0.256 3252 -
obs--99.27 %

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