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- PDB-5eke: Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB... -

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Basic information

Entry
Database: PDB / ID: 5eke
TitleStructure of the polyisoprenyl-phosphate glycosyltransferase GtrB (F215A mutant)
ComponentsUncharacterized glycosyltransferase sll0501
KeywordsTRANSFERASE / glycosyltransferase / membrane protein / enzyme / bactoprenol / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
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 / SAD / Resolution: 3.001 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)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111980 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095315 United States
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 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)158,68712
Polymers156,9734
Non-polymers1,7148
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17260 Å2
ΔGint-185 kcal/mol
Surface area55130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.135, 142.243, 102.010
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized glycosyltransferase sll0501


Mass: 39243.336 Da / Num. of mol.: 4 / Mutation: F215A
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


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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 600 nL protein + 300 nL of reservoir composed as follows: containing 16-18% PEG600 (v/v), 0.12 M Tris/HCl, pH 9.0, 0.1 M NaCl and 1 mM TCEP) under 1 uL of silicone oil, in 96-well Axygen ...Details: 600 nL protein + 300 nL of reservoir composed as follows: containing 16-18% PEG600 (v/v), 0.12 M Tris/HCl, pH 9.0, 0.1 M NaCl and 1 mM TCEP) under 1 uL of silicone oil, in 96-well Axygen sitting-drop plates. Crystals typically appeared after 1-2 days and grew to a final size of approximately 150 um in each dimension

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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: May 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→34.384 Å / Num. obs: 43376 / % possible obs: 99.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 112.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.025 / Net I/σ(I): 19.1 / Num. measured all: 182807 / Scaling rejects: 15
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3-3.114.21.2631.11883244670.6930.69697.8
11.23-34.383.90.02666.232568310.9970.01595.4

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Processing

Software
NameVersionClassification
PHENIXdev_2165refinement
Aimless0.5.14data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.001→34.384 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 2058 4.79 %
Rwork0.2486 --
obs0.25 42993 98.56 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.001→34.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9136 0 104 0 9240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099455
X-RAY DIFFRACTIONf_angle_d0.53112888
X-RAY DIFFRACTIONf_dihedral_angle_d13.5925531
X-RAY DIFFRACTIONf_chiral_restr0.0421513
X-RAY DIFFRACTIONf_plane_restr0.0051606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0015-3.07130.43121060.41062657X-RAY DIFFRACTION95
3.0713-3.1480.36581420.33892734X-RAY DIFFRACTION100
3.148-3.23310.34551300.32262760X-RAY DIFFRACTION100
3.2331-3.32810.44021540.32822727X-RAY DIFFRACTION100
3.3281-3.43550.32081250.30442756X-RAY DIFFRACTION100
3.4355-3.55810.35891350.31012757X-RAY DIFFRACTION99
3.5581-3.70040.31451370.28542710X-RAY DIFFRACTION99
3.7004-3.86860.31311390.25622764X-RAY DIFFRACTION99
3.8686-4.07230.28031300.25412682X-RAY DIFFRACTION97
4.0723-4.3270.25561420.22842675X-RAY DIFFRACTION97
4.327-4.66030.2251230.20492728X-RAY DIFFRACTION98
4.6603-5.12790.24611400.22022746X-RAY DIFFRACTION99
5.1279-5.86680.2811330.2442743X-RAY DIFFRACTION99
5.8668-7.37950.33371600.25722736X-RAY DIFFRACTION99
7.3795-34.38640.22471620.22892760X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -54.5789 Å / Origin y: 24.8206 Å / Origin z: 15.7268 Å
111213212223313233
T0.7656 Å20.0582 Å2-0.0011 Å2-0.7578 Å2-0.0603 Å2--0.78 Å2
L1.2862 °20.1147 °20.3379 °2-0.9858 °2-0.1859 °2--1.6337 °2
S-0.2028 Å °-0.1239 Å °0.1775 Å °0.2223 Å °0.091 Å °-0.2994 Å °-0.0437 Å °0.4468 Å °0.0846 Å °
Refinement TLS groupSelection details: all

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