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- PDB-5xhp: Transferase with ligands -

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Basic information

Entry
Database: PDB / ID: 5xhp
TitleTransferase with ligands
ComponentsPutative cytoplasmic protein
KeywordsTRANSFERASE / Glycosyltransferase / UDP and L-Arginine bounded enzyme
Function / homologynucleotide binding / metal ion binding / ARGININE / : / URIDINE-5'-DIPHOSPHATE / Cytoplasmic protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsPark, J. / Yoo, Y. / Kim, Y.H. / Cho, H.S.
CitationJournal: To Be Published
Title: Crystal structure of L-arginine and UDP bounded glycosyltransfease
Authors: Park, J. / Yoo, Y. / Cho, H.S.
History
DepositionApr 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Putative cytoplasmic protein
E: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5028
Polymers79,2342
Non-polymers1,2696
Water00
1
F: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2514
Polymers39,6171
Non-polymers6343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-13 kcal/mol
Surface area14390 Å2
MethodPISA
2
E: Putative cytoplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2514
Polymers39,6171
Non-polymers6343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-13 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.116, 50.116, 201.704
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Putative cytoplasmic protein


Mass: 39616.930 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / 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: 1.85 Å3/Da / Density % sol: 33.36 %
Crystal growTemperature: 290 K / Method: evaporation / 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: CCD / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13266 / % possible obs: 99.8 % / Redundancy: 7.6 % / Net I/σ(I): 2.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementResolution: 2.8→43.402 Å / Cor.coef. Fo:Fc: 0.855 / Cor.coef. Fo:Fc free: 0.771 / SU B: 29.699 / SU ML: 0.592 / Cross valid method: THROUGHOUT / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31864 675 4.8 %RANDOM
Rwork0.28842 ---
obs0.28994 13266 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.643 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.8→43.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 76 0 4960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195076
X-RAY DIFFRACTIONr_bond_other_d0.0040.024590
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9686872
X-RAY DIFFRACTIONr_angle_other_deg1.138310704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9745604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.79924.844256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.04115880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2641522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215610
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021012
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_it3.5346.7562428
X-RAY DIFFRACTIONr_mcbond_other3.5356.7572427
X-RAY DIFFRACTIONr_mcangle_it5.57510.1233028
X-RAY DIFFRACTIONr_mcangle_other5.57410.1233029
X-RAY DIFFRACTIONr_scbond_it3.1646.9172648
X-RAY DIFFRACTIONr_scbond_other3.1646.9172647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.07610.3113845
X-RAY DIFFRACTIONr_long_range_B_refined9.9921380
X-RAY DIFFRACTIONr_long_range_B_other9.9921381
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.797→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 32 -
Rwork0.346 938 -
obs--97.59 %

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