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- PDB-6j31: Crystal Structure Analysis of the Glycotransferase of kitacinnamycin -

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Basic information

Entry
Database: PDB / ID: 6j31
TitleCrystal Structure Analysis of the Glycotransferase of kitacinnamycin
Components
  • DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
  • kcn28
KeywordsBIOSYNTHETIC PROTEIN / Glycotransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity
Similarity search - Function
UDP-glycosyltransferase, MGT-like / 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
Chem-BG9 / Glycosyltransferase
Similarity search - Component
Biological speciesKitasatospora (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.244 Å
AuthorsShi, J. / Liu, C.L. / Zhang, B. / Guo, W.J. / Zhu, J.P. / Xu, X. / Xu, Q. / Jiao, R.H. / Tan, R.X. / Ge, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)81522042, 21572100, 81773591, 81530089, 81673333, 81803380, 21861142005, 21761142001, 21661140001 China
CitationJournal: Chem Sci / Year: 2019
Title: Genome mining and biosynthesis of kitacinnamycins as a STING activator.
Authors: Shi, J. / Liu, C.L. / Zhang, B. / Guo, W.J. / Zhu, J. / Chang, C.Y. / Zhao, E.J. / Jiao, R.H. / Tan, R.X. / Ge, H.M.
History
DepositionJan 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: kcn28
B: kcn28
C: kcn28
D: kcn28
E: DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
F: DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
G: DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
H: DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,83412
Polymers176,9618
Non-polymers8734
Water10,196566
1
A: kcn28
E: DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4583
Polymers44,2402
Non-polymers2181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-9 kcal/mol
Surface area17310 Å2
MethodPISA
2
B: kcn28
F: DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4583
Polymers44,2402
Non-polymers2181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-10 kcal/mol
Surface area17610 Å2
MethodPISA
3
C: kcn28
G: DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4583
Polymers44,2402
Non-polymers2181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-11 kcal/mol
Surface area17580 Å2
MethodPISA
4
D: kcn28
H: DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4583
Polymers44,2402
Non-polymers2181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-10 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)243.160, 243.160, 243.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 134 or (resid 135...
21(chain B and (resid 2 through 62 or resid 72...
31(chain C and (resid 2 through 62 or resid 72 through 401))
41(chain D and (resid 2 through 62 or resid 72...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPRO(chain A and (resid 2 through 134 or (resid 135...AA2 - 1342 - 134
12GLUGLUGLUGLU(chain A and (resid 2 through 134 or (resid 135...AA135135
13PROPROHOHHOH(chain A and (resid 2 through 134 or (resid 135...AA - M2 - 4012
14PROPROHOHHOH(chain A and (resid 2 through 134 or (resid 135...AA - M2 - 4012
15PROPROHOHHOH(chain A and (resid 2 through 134 or (resid 135...AA - M2 - 4012
16PROPROHOHHOH(chain A and (resid 2 through 134 or (resid 135...AA - M2 - 4012
21PROPROPROPRO(chain B and (resid 2 through 62 or resid 72...BB2 - 622 - 62
22THRTHRPROPRO(chain B and (resid 2 through 62 or resid 72...BB72 - 13472 - 134
23METMETHOHHOH(chain B and (resid 2 through 62 or resid 72...BB - N1 - 4011
24METMETHOHHOH(chain B and (resid 2 through 62 or resid 72...BB - N1 - 4011
25METMETHOHHOH(chain B and (resid 2 through 62 or resid 72...BB - N1 - 4011
26METMETHOHHOH(chain B and (resid 2 through 62 or resid 72...BB - N1 - 4011
27METMETHOHHOH(chain B and (resid 2 through 62 or resid 72...BB - N1 - 4011
28METMETHOHHOH(chain B and (resid 2 through 62 or resid 72...BB - N1 - 4011
29METMETHOHHOH(chain B and (resid 2 through 62 or resid 72...BB - N1 - 4011
31PROPROPROPRO(chain C and (resid 2 through 62 or resid 72 through 401))CC2 - 622 - 62
32THRTHRHOHHOH(chain C and (resid 2 through 62 or resid 72 through 401))CC - O72 - 40172
41PROPROPROPRO(chain D and (resid 2 through 62 or resid 72...DD2 - 622 - 62
42THRTHRPROPRO(chain D and (resid 2 through 62 or resid 72...DD72 - 13472 - 134
43GLUGLUGLUGLU(chain D and (resid 2 through 62 or resid 72...DD135135
44PROPROHOHHOH(chain D and (resid 2 through 62 or resid 72...DD - P2 - 4012
45PROPROHOHHOH(chain D and (resid 2 through 62 or resid 72...DD - P2 - 4012
46PROPROHOHHOH(chain D and (resid 2 through 62 or resid 72...DD - P2 - 4012

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Components

#1: Protein
kcn28


Mass: 43337.152 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kitasatospora (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A514S208*PLUS
#2: Protein/peptide
DBB-DSG-VAL-MEA-VAL-GLY-GLY-DVA-DLE / kitacinnamycin


Mass: 903.077 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-BG9 / (2E,2'E)-3,3'-(1,2-phenylene)di(prop-2-enoic acid)


Mass: 218.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H10O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 3.46 Å3/Da / Density % sol: 64.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 1.6 M Ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 10% v/v 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.24→39.45 Å / Num. obs: 113347 / % possible obs: 100 % / Redundancy: 19 % / CC1/2: 0.998 / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.062 / Rrim(I) all: 0.272 / Net I/σ(I): 8.3 / Num. measured all: 2156843 / Scaling rejects: 1051
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.24-2.2819.81.97256290.1790.4542.024100
12.29-39.4518.90.0667280.9990.0160.06897.2

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IYF

2iyf


Resolution: 2.244→39.446 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.59
RfactorNum. reflection% reflection
Rfree0.2485 5489 4.84 %
Rwork0.2257 --
obs0.2268 113311 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 181.82 Å2 / Biso mean: 56.4916 Å2 / Biso min: 24.58 Å2
Refinement stepCycle: final / Resolution: 2.244→39.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11910 0 312 566 12788
Biso mean--71.92 47.8 -
Num. residues----1546
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7422X-RAY DIFFRACTION18.827TORSIONAL
12B7422X-RAY DIFFRACTION18.827TORSIONAL
13C7422X-RAY DIFFRACTION18.827TORSIONAL
14D7422X-RAY DIFFRACTION18.827TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2444-2.26990.42261670.393536333800
2.2699-2.29660.35751750.370535593734
2.2966-2.32460.38761910.362436103801
2.3246-2.3540.36841550.346735553710
2.354-2.3850.34132130.343235283741
2.385-2.41760.37522260.336335783804
2.4176-2.45220.36272050.331135343739
2.4522-2.48880.32822100.315835833793
2.4888-2.52770.28931670.303735163683
2.5277-2.56910.29761570.298936363793
2.5691-2.61340.32082110.296735533764
2.6134-2.66090.27762140.2835403754
2.6609-2.71210.27531800.256835633743
2.7121-2.76740.29912040.264935743778
2.7674-2.82760.33641870.285335683755
2.8276-2.89330.28231770.268136003777
2.8933-2.96560.26231860.250635993785
2.9656-3.04580.25351760.247235833759
3.0458-3.13540.24541820.236135463728
3.1354-3.23650.24631650.231236283793
3.2365-3.35220.25851990.238435733772
3.3522-3.48630.2461580.218336243782
3.4863-3.64490.23831550.198336003755
3.6449-3.83690.24061600.201336203780
3.8369-4.0770.22011610.186236433804
4.077-4.39150.19641490.167936503799
4.3915-4.83270.17021720.160636313803
4.8327-5.53040.18072120.179536213833
5.5304-6.96140.22171800.200336403820
6.9614-39.45180.19081950.160737343929
Refinement TLS params.Method: refined / Origin x: 35.6962 Å / Origin y: 107.9266 Å / Origin z: 82.8508 Å
111213212223313233
T0.3056 Å2-0.0067 Å2-0.0145 Å2-0.2858 Å20.0013 Å2--0.3615 Å2
L0.305 °20.203 °2-0.0624 °2-0.3073 °20.043 °2--0.2355 °2
S-0.011 Å °0.01 Å °-0.0412 Å °-0.0331 Å °-0.0041 Å °-0.0736 Å °0.0271 Å °0.019 Å °0.0103 Å °
Refinement TLS groupSelection details: all

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