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- PDB-5xyk: Structure of Transferase -

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Basic information

Entry
Database: PDB / ID: 5xyk
TitleStructure of Transferase
ComponentsPutative cytoplasmic protein
KeywordsTRANSFERASE
Function / homology
Function and homology information


protein-arginine N-acetylglucosaminyltransferase activity / host cell / toxin activity / nucleotide binding / extracellular region / metal ion binding
Similarity search - Function
ARGININE / : / URIDINE-5'-DIPHOSPHATE / Cytoplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsPark, J.B. / Yoo, Y. / Kim, J. / Cho, H.S.
CitationJournal: To Be Published
Title: Structure of Transferase
Authors: Park, J.B. / Yoo, Y. / Kim, J. / Cho, H.S.
History
DepositionJul 9, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2514
Polymers39,6171
Non-polymers6343
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-13 kcal/mol
Surface area14270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.059, 50.059, 201.242
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Putative cytoplasmic protein


Mass: 39616.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain 4/74) (bacteria)
Strain: 4/74 / Gene: STM474_2223 / Production host: Escherichia coli (E. coli) / References: UniProt: E8XCX6
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM

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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: 1.84 Å3/Da / Density % sol: 33.05 %
Crystal growTemperature: 290 K / Method: evaporation, recrystallization / pH: 5.5
Details: 0.2M ammonium acetate 0.1M Bis-Tris pH5.5 25% PEG2250

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→67.08 Å / Num. obs: 9052 / % possible obs: 94.87 % / Redundancy: 7.6 % / Net I/σ(I): 3.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H5Y

5h5y


Resolution: 2.57→67.08 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.822 / SU B: 14.817 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28586 457 4.8 %RANDOM
Rwork0.2612 ---
obs0.26242 9052 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.524 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.57→67.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 38 0 2480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192538
X-RAY DIFFRACTIONr_bond_other_d0.0060.022295
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9683436
X-RAY DIFFRACTIONr_angle_other_deg1.09735352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.855302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.03624.844128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96215440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6091511
X-RAY DIFFRACTIONr_chiral_restr0.1070.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212805
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02506
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_it2.0153.1471214
X-RAY DIFFRACTIONr_mcbond_other2.0153.1471213
X-RAY DIFFRACTIONr_mcangle_it3.2284.7121514
X-RAY DIFFRACTIONr_mcangle_other3.2274.7131515
X-RAY DIFFRACTIONr_scbond_it2.043.2991324
X-RAY DIFFRACTIONr_scbond_other2.043.2991325
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2844.8771923
X-RAY DIFFRACTIONr_long_range_B_refined6.59158.9610701
X-RAY DIFFRACTIONr_long_range_B_other6.59158.95810701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.569→2.635 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 18 -
Rwork0.315 475 -
obs--66.26 %

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