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- PDB-3nyt: X-ray crystal structure of the WlbE (WpbE) aminotransferase from ... -

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Basic information

Entry
Database: PDB / ID: 3nyt
TitleX-ray crystal structure of the WlbE (WpbE) aminotransferase from pseudomonas aeruginosa, mutation K185A, in complex with the PLP external aldimine adduct with UDP-3-amino-2-N-acetyl-glucuronic acid, at 1.3 angstrom resolution
ComponentsAminotransferase WbpE
KeywordsTRANSFERASE / aminotransferase / PLP binding / nucleotide-sugar binding
Function / homology
Function and homology information


UDP-2-acetamido-2-deoxy-ribo-hexuluronate aminotransferase / UDP-glucuronate biosynthetic process / O antigen biosynthetic process / lipopolysaccharide biosynthetic process / polysaccharide 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
Chem-ULP / UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.301 Å
AuthorsHolden, H.M. / Thoden, J.B.
CitationJournal: Protein Sci. / Year: 2017
Title: Structural investigation on WlaRG from Campylobacter jejuni: A sugar aminotransferase.
Authors: Dow, G.T. / Gilbert, M. / Thoden, J.B. / Holden, H.M.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Mar 29, 2017Group: Database references
Revision 1.4Sep 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 / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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: Aminotransferase WbpE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8513
Polymers39,9791
Non-polymers8722
Water8,467470
1
A: Aminotransferase WbpE
hetero molecules

A: Aminotransferase WbpE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7026
Polymers79,9572
Non-polymers1,7454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5370 Å2
ΔGint-54 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.684, 92.170, 75.652
Angle α, β, γ (deg.)90.00, 111.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-369-

NA

21A-557-

HOH

31A-588-

HOH

41A-683-

HOH

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Components

#1: Protein Aminotransferase WbpE


Mass: 39978.586 Da / Num. of mol.: 1 / Mutation: K185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3155, wbpE / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9HZ76
#2: Chemical ChemComp-ULP / (2S,3S,4R,5R,6R)-5-(acetylamino)-6-{[(R)-{[(S)-{[(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-hydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}tetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)


Mass: 849.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H34N5O22P3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% pentaerythritol propoxylate, 100 mM MES, 50mM UDP-3-amino-20N-acetyl-glucuronic acid, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jan 1, 2010 / Details: montel
RadiationMonochromator: Ni-filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 90696 / Num. obs: 90696 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 15.8
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / Num. unique all: 3399 / Rsym value: 0.33 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
REFMAC5.5.0066refinement
SAINTdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NYS

3nys


Resolution: 1.301→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 0.9 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.053 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21626 4537 5 %RANDOM
Rwork0.18964 ---
all0.19097 90693 --
obs0.19097 86156 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.137 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.61 Å2
2--0.03 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.301→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 56 470 3255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222854
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.181.9983896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32524.661118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57615465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3421516
X-RAY DIFFRACTIONr_chiral_restr0.1460.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212146
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_it1.5191.51799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.28822906
X-RAY DIFFRACTIONr_scbond_it3.51531055
X-RAY DIFFRACTIONr_scangle_it5.4554.5987
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 284 -
Rwork0.364 5827 -
obs--89.96 %

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