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- PDB-4ztc: PglE Aminotransferase in complex with External Aldimine, Mutant K184A -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4ztc
TitlePglE Aminotransferase in complex with External Aldimine, Mutant K184A
ComponentsAminotransferase homolog
KeywordsTRANSFERASE / aminotransferase / N-N'-diacetylbacillosamine / N-glycosylation pyridoxyl 5'-phosphate
Function / homology
Function and homology information


UDP-N-acetylbacillosamine transaminase / UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose transaminase activity / polysaccharide biosynthetic process / : / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-4RA / UDP-N-acetylbacillosamine transaminase / Aminotransferase homolog
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRiegert, A.S. / Thoden, J.B. / Young, N.M. / Watson, D.C. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2015
Title: Structure of the external aldimine form of PglE, an aminotransferase required for N,N'-diacetylbacillosamine biosynthesis.
Authors: Riegert, A.S. / Young, N.M. / Watson, D.C. / Thoden, J.B. / Holden, H.M.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6192
Polymers43,7991
Non-polymers8191
Water4,954275
1
A: Aminotransferase homolog
hetero molecules

A: Aminotransferase homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,2374
Polymers87,5982
Non-polymers1,6392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5650 Å2
ΔGint-34 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.161, 66.161, 169.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-716-

HOH

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Components

#1: Protein Aminotransferase homolog


Mass: 43799.203 Da / Num. of mol.: 1 / Mutation: K184A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Plasmid: pET28t / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9S5Y7, UniProt: Q0P9D3*PLUS
#2: Chemical ChemComp-4RA / [(2R,3R,4R,5S,6R)-3-acetamido-6-methyl-5-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-4-oxidanyl-oxan-2-yl] [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 819.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H36N5O20P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe sequence differences are substrain specific

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-18% PEG3350, 1 mM PLP, 10 mM UDP-2-acetamido-4-amino-2,4,6-trideoxyglucose, 100 mM MOPS, 200 mM tetraethylammoniumchloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 26017 / Num. obs: 26017 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/av σ(I): 15.1 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.8 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1O61

1o61


Resolution: 2→29.61 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.242 / SU ML: 0.147 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25445 1330 5.1 %RANDOM
Rwork0.18835 ---
obs0.19184 24687 99.06 %-
all-26017 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.058 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.73 Å2
Refinement stepCycle: 1 / Resolution: 2→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 53 275 3403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193205
X-RAY DIFFRACTIONr_bond_other_d0.0010.023087
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.9884329
X-RAY DIFFRACTIONr_angle_other_deg0.82437128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9435388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.89225.034145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66215593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8581512
X-RAY DIFFRACTIONr_chiral_restr0.0940.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023565
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 97 -
Rwork0.226 1727 -
obs--96.46 %

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