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- PDB-5nlm: Complex between a UDP-glucosyltransferase from Polygonum tinctori... -

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Basic information

Entry
Database: PDB / ID: 5nlm
TitleComplex between a UDP-glucosyltransferase from Polygonum tinctorium capable of glucosylating indoxyl and indoxyl sulfate
Componentsindoxyl UDP-glucosyltransferase
KeywordsTRANSFERASE / UDPglucose:indoxyl glucosyltransferase GT-B UGT indigo
Function / homology
Function and homology information


UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-SULFOOXY-1H-INDOLE / Glycosyltransferase
Similarity search - Component
Biological speciesPersicaria tinctoria (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsWelner, D.H. / Hsu, T. / Dueber, J. / Adams, P.D.
Funding support United States, 4items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
Bakar Fellows Program United States
National Science Foundation (NSF, United States)1605465 United States
Department of Defense (DOD, United States) United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Employing a biochemical protecting group for a sustainable indigo dyeing strategy.
Authors: Hsu, T.M. / Welner, D.H. / Russ, Z.N. / Cervantes, B. / Prathuri, R.L. / Adams, P.D. / Dueber, J.E.
History
DepositionApr 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: indoxyl UDP-glucosyltransferase
B: indoxyl UDP-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,3579
Polymers103,8092
Non-polymers5487
Water1,874104
1
A: indoxyl UDP-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2156
Polymers51,9041
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: indoxyl UDP-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1423
Polymers51,9041
Non-polymers2382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.000, 172.820, 48.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein indoxyl UDP-glucosyltransferase


Mass: 51904.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Persicaria tinctoria (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: A0A2R2JFJ4*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-IOS / 3-SULFOOXY-1H-INDOLE / Indoxyl sulfate


Mass: 213.210 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO4S / Comment: toxin*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2M MgCl2*6H20, 0.1 M Hepes pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2016
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.14→48.41 Å / Num. obs: 55926 / % possible obs: 97.97 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.08972 / Net I/σ(I): 15.58
Reflection shellResolution: 2.14→2.216 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.519 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 4759 / CC1/2: 0.327 / % possible all: 84.44

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vce
Resolution: 2.14→48.41 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.21
RfactorNum. reflection% reflection
Rfree0.2521 2780 4.97 %
Rwork0.2254 --
obs0.2268 55921 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.14→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6986 0 33 104 7123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027193
X-RAY DIFFRACTIONf_angle_d0.5169776
X-RAY DIFFRACTIONf_dihedral_angle_d10.6894341
X-RAY DIFFRACTIONf_chiral_restr0.0411099
X-RAY DIFFRACTIONf_plane_restr0.0041264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.17690.38771130.35632162X-RAY DIFFRACTION81
2.1769-2.21650.41621230.34242361X-RAY DIFFRACTION88
2.2165-2.25910.35021270.33522506X-RAY DIFFRACTION95
2.2591-2.30520.36061190.31562645X-RAY DIFFRACTION96
2.3052-2.35540.31011380.29822614X-RAY DIFFRACTION100
2.3554-2.41010.29751490.28662706X-RAY DIFFRACTION100
2.4101-2.47040.32081470.27982642X-RAY DIFFRACTION100
2.4704-2.53720.29581410.26392683X-RAY DIFFRACTION100
2.5372-2.61190.2851420.25222676X-RAY DIFFRACTION100
2.6119-2.69620.30091250.26282724X-RAY DIFFRACTION100
2.6962-2.79250.31231320.26162670X-RAY DIFFRACTION100
2.7925-2.90430.27651420.26342696X-RAY DIFFRACTION100
2.9043-3.03650.30381430.26062725X-RAY DIFFRACTION100
3.0365-3.19650.2711300.25722705X-RAY DIFFRACTION100
3.1965-3.39680.28831650.25752664X-RAY DIFFRACTION100
3.3968-3.6590.2641560.23252728X-RAY DIFFRACTION100
3.659-4.0270.22391540.19732738X-RAY DIFFRACTION100
4.027-4.60940.19281450.16832744X-RAY DIFFRACTION100
4.6094-5.80590.19151440.17612799X-RAY DIFFRACTION100
5.8059-49.57330.21341450.19152953X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.6199-1.35052.09083.0431-2.06483.93860.1672-0.2520.5830.0867-0.148-0.0705-0.23470.2274-0.00860.3025-0.01350.01990.3314-0.10330.3815-36.366951.95723.1742
27.01090.2383-1.06772.75380.13451.9186-0.0272-0.4494-0.25650.1841-0.01180.01830.19890.08970.05450.2813-0.0219-0.03220.2790.00850.1816-33.989439.37882.927
36.43441.20220.07953.73850.24941.4422-0.10460.39010.1658-0.22470.1687-0.45740.08290.1711-0.04420.2776-0.02210.06880.34870.00470.2822-19.33644.9199-6.0181
48.1184-0.75630.79333.41-0.04192.17450.0105-1.06860.5770.34230.0177-0.2541-0.04310.0298-0.04030.2695-0.02970.03760.4592-0.12240.4107-4.538249.7946.0761
58.80771.1758-0.15181.0462-0.52412.34740.27261.60443.0277-0.2177-0.01830.2218-0.5996-0.0879-0.06590.61020.03930.00650.44230.27770.9536-23.177259.4397-10.0723
63.71920.61370.45927.59841.6323.32550.0453-0.00230.80540.6462-0.39350.4909-0.6141-0.24730.35030.5579-0.01840.01440.3498-0.02260.6909-42.286381.777218.1827
75.6073-1.3391-1.31091.9808-1.19747.36360.18450.35070.77150.6012-0.0471-0.8816-1.37560.1056-0.08770.8713-0.0301-0.03490.50720.15641.3505-16.821498.80839.0461
86.72914.38410.1376.1576-0.03464.22820.0442-0.2508-0.23491.3801-0.0353-1.3174-0.61170.731-0.01550.934-0.0379-0.31220.51640.04291.0389-23.435485.20124.3478
98.21511.99952.00061.99891.99922.0004-0.02010.12470.11370.75830.1346-0.1288-0.8379-0.28420.01751.345-0.79030.022.07210.10780.7783-20.603339.5610.8298
108.0880.3484-2.3563.8408-0.28641.99921.21170.14310.5186-0.1947-0.95210.2846-0.2896-0.0016-0.24731.4085-0.09950.37971.5985-0.43132.6257-38.462389.794317.9421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 163 )
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 279 )
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 436 )
5X-RAY DIFFRACTION5chain 'A' and (resid 437 through 477 )
6X-RAY DIFFRACTION6chain 'B' and (resid 9 through 274 )
7X-RAY DIFFRACTION7chain 'B' and (resid 275 through 355 )
8X-RAY DIFFRACTION8chain 'B' and (resid 356 through 477 )
9X-RAY DIFFRACTION9chain 'A' and resid 1002
10X-RAY DIFFRACTION10chain 'B' and resid 1001

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