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- PDB-5f87: Crystal structure of Drosophila Poglut1 (Rumi) complexed with UDP -

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Basic information

Entry
Database: PDB / ID: 5f87
TitleCrystal structure of Drosophila Poglut1 (Rumi) complexed with UDP
ComponentsO-glucosyltransferase rumi
KeywordsTRANSFERASE / glycosyltransferase / protein O-glucosyltransferase / Notch regulation / EGF repeat
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / rhabdomere development / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / UDP-glucosyltransferase activity / glucosyltransferase activity / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases ...EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / rhabdomere development / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / UDP-glucosyltransferase activity / glucosyltransferase activity / protein O-linked glycosylation / Transferases; Glycosyltransferases; Hexosyltransferases / positive regulation of Notch signaling pathway / negative regulation of Notch signaling pathway / endomembrane system / cell fate commitment / Notch signaling pathway / endoplasmic reticulum lumen
Similarity search - Function
Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Endoplasmic reticulum targeting sequence.
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / O-glucosyltransferase rumi
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 Å
AuthorsYu, H.J. / Li, H.L.
CitationJournal: Nat. Chem. Biol. / Year: 2016
Title: Structural analysis of Notch-regulating Rumi reveals basis for pathogenic mutations.
Authors: Yu, H. / Takeuchi, H. / Takeuchi, M. / Liu, Q. / Kantharia, J. / Haltiwanger, R.S. / Li, H.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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: O-glucosyltransferase rumi
B: O-glucosyltransferase rumi
C: O-glucosyltransferase rumi
D: O-glucosyltransferase rumi
E: O-glucosyltransferase rumi
F: O-glucosyltransferase rumi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,89918
Polymers280,9216
Non-polymers2,97812
Water0
1
A: O-glucosyltransferase rumi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3163
Polymers46,8201
Non-polymers4962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: O-glucosyltransferase rumi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3163
Polymers46,8201
Non-polymers4962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: O-glucosyltransferase rumi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3163
Polymers46,8201
Non-polymers4962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: O-glucosyltransferase rumi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3163
Polymers46,8201
Non-polymers4962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: O-glucosyltransferase rumi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3163
Polymers46,8201
Non-polymers4962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: O-glucosyltransferase rumi
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3163
Polymers46,8201
Non-polymers4962
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)241.908, 241.908, 47.315
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A42 - 406
2010B42 - 406
1020A42 - 406
2020C42 - 406
1030A42 - 406
2030D42 - 406
1040A42 - 406
2040E42 - 406
1050A42 - 406
2050F42 - 406
1060B42 - 406
2060C42 - 406
1070B42 - 406
2070D42 - 406
1080B42 - 406
2080E42 - 406
1090B42 - 406
2090F42 - 406
10100C42 - 406
20100D42 - 406
10110C42 - 406
20110E42 - 406
10120C42 - 406
20120F42 - 406
10130D42 - 406
20130E42 - 406
10140D42 - 406
20140F42 - 406
10150E42 - 406
20150F42 - 406

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
O-glucosyltransferase rumi


Mass: 46820.172 Da / Num. of mol.: 6 / Fragment: UNP residues 21-407
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: rumi, CG31152 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: Q8T045, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH7.4, 1.2M sodium citrate tribasic, 6% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.496
11-K, -H, -L20.504
ReflectionResolution: 3.2→50 Å / Num. obs: 50868 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.158 / Net I/σ(I): 6.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 1.8 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementResolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.819 / SU B: 16.459 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20256 2585 5.2 %RANDOM
Rwork0.1684 ---
obs0.17016 47545 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.677 Å2
Baniso -1Baniso -2Baniso -3
1-10.48 Å20 Å20 Å2
2--10.48 Å20 Å2
3----20.96 Å2
Refinement stepCycle: 1 / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18144 0 186 0 18330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218894
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.95625566
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71752184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93522.893954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.423153216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.35715156
X-RAY DIFFRACTIONr_chiral_restr0.0830.22550
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114586
X-RAY DIFFRACTIONr_gen_planes_other
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A505
12B505
21A509
22C509
31A507
32D507
41A504
42E504
51A507
52F507
61B511
62C511
71B507
72D507
81B506
82E506
91B513
92F513
101C508
102D508
111C508
112E508
121C509
122F509
131D503
132E503
141D510
142F510
151E505
152F505
LS refinement shellResolution: 3.202→3.285 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 173 -
Rwork0.205 3044 -
obs--85.44 %

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