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- PDB-5ekp: Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB (WT) -

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Basic information

Entry
Database: PDB / ID: 5ekp
TitleStructure of the polyisoprenyl-phosphate glycosyltransferase GtrB (WT)
ComponentsUncharacterized glycosyltransferase sll0501
KeywordsTRANSFERASE / glycosyltransferase / membrane protein / enzyme / bactoprenol
Function / homologyTransferases; Glycosyltransferases / Glycosyltransferase 2-like / Glycosyl transferase family 2 / glycosyltransferase activity / Nucleotide-diphospho-sugar transferases / plasma membrane / URIDINE-5'-DIPHOSPHATE / Uncharacterized glycosyltransferase sll0501
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.194 Å
AuthorsArdiccioni, C. / Clarke, O.B. / Tomasek, D. / Banerjee, S. / Rajashankar, K.R. / Liu, Q. / Shapiro, L. / Mancia, F. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis.
Authors: Ardiccioni, C. / Clarke, O.B. / Tomasek, D. / Issa, H.A. / von Alpen, D.C. / Pond, H.L. / Banerjee, S. / Rajashankar, K.R. / Liu, Q. / Guan, Z. / Li, C. / Kloss, B. / Bruni, R. / Kloppmann, ...Authors: Ardiccioni, C. / Clarke, O.B. / Tomasek, D. / Issa, H.A. / von Alpen, D.C. / Pond, H.L. / Banerjee, S. / Rajashankar, K.R. / Liu, Q. / Guan, Z. / Li, C. / Kloss, B. / Bruni, R. / Kloppmann, E. / Rost, B. / Manzini, M.C. / Shapiro, L. / Mancia, F.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Uncharacterized glycosyltransferase sll0501
A: Uncharacterized glycosyltransferase sll0501
B: Uncharacterized glycosyltransferase sll0501
D: Uncharacterized glycosyltransferase sll0501
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,99212
Polymers157,2784
Non-polymers1,7148
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17130 Å2
ΔGint-183 kcal/mol
Surface area54890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.331, 137.518, 101.448
Angle α, β, γ (deg.)90.000, 98.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized glycosyltransferase sll0501


Mass: 39319.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll0501 / Production host: Escherichia coli (E. coli)
References: UniProt: Q55487, Transferases; Glycosyltransferases
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 3.45 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 16-18% PEG600 (v/v), 0.12 M Tris/HCl, pH 9.0, 0.1 M NaCl and 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→19.988 Å / Num. obs: 36869 / % possible obs: 96.9 % / Redundancy: 2.6 % / Biso Wilson estimate: 126.12 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.04 / Net I/σ(I): 12.8 / Num. measured all: 97120 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.1-3.242.61.2460.81176345030.4160.93596.9
10.75-48.322.50.03151.221428620.9940.02691.2

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Processing

Software
NameVersionClassification
PHENIXdev_2210refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementResolution: 3.194→19.988 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.291 1724 4.94 %
Rwork0.2479 33151 -
obs0.2501 34875 98.7 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 439.61 Å2 / Biso mean: 165.924 Å2 / Biso min: 50 Å2
Refinement stepCycle: final / Resolution: 3.194→19.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9136 0 104 0 9240
Biso mean--161.63 --
Num. residues----1190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019453
X-RAY DIFFRACTIONf_angle_d0.51712885
X-RAY DIFFRACTIONf_chiral_restr0.0411513
X-RAY DIFFRACTIONf_plane_restr0.0051606
X-RAY DIFFRACTIONf_dihedral_angle_d16.8433296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1943-3.28790.41311460.36122676282296
3.2879-3.39350.41311650.329127622927100
3.3935-3.51410.33921480.320327632911100
3.5141-3.6540.38721370.300827932930100
3.654-3.81920.33191340.286628032937100
3.8192-4.01910.32251750.25962746292199
4.0191-4.26860.27951370.2542774291199
4.2686-4.59450.27871520.22362772292499
4.5945-5.050.26681260.21712780290699
5.05-5.76540.2641240.24142810293499
5.7654-7.20680.31471260.275128292955100
7.2068-19.98860.25721540.21422643279793

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