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- PDB-3nys: X-ray structure of the K185A mutant of WbpE (WlbE) from pseudomon... -

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Basic information

Entry
Database: PDB / ID: 3nys
TitleX-ray structure of the K185A mutant of WbpE (WlbE) from pseudomonas aeruginosa in complex with PLP at 1.45 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 / 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
PYRIDOXAL-5'-PHOSPHATE / UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 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 / 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)40,2493
Polymers39,9791
Non-polymers2702
Water8,737485
1
A: Aminotransferase WbpE
hetero molecules

A: Aminotransferase WbpE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4976
Polymers79,9572
Non-polymers5404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area5330 Å2
ΔGint-24 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.783, 93.570, 77.067
Angle α, β, γ (deg.)90.00, 115.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-369-

NA

21A-577-

HOH

31A-579-

HOH

41A-635-

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): Resetta2(DE3) / References: UniProt: Q9HZ76
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#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.: 485 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% pentaerythritrol propoxylate, 100 mM MES, 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: Feb 22, 2010 / Details: mondel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 62362 / Num. obs: 62362 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2316 / Rsym value: 0.32 / % possible all: 92.9

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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 3FRK

3frk


Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.148 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20085 3163 5.1 %RANDOM
Rwork0.17002 ---
all0.17161 62330 --
obs0.17161 59196 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.169 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å20.35 Å2
2--0.05 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2729 0 17 485 3231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222809
X-RAY DIFFRACTIONr_angle_refined_deg2.0031.9823824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58824.615117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30715467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8771516
X-RAY DIFFRACTIONr_chiral_restr0.1440.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212115
X-RAY DIFFRACTIONr_mcbond_it1.5981.51796
X-RAY DIFFRACTIONr_mcangle_it2.40522901
X-RAY DIFFRACTIONr_scbond_it3.61131013
X-RAY DIFFRACTIONr_scangle_it5.3124.5921
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 207 -
Rwork0.248 4103 -
obs--91.7 %

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