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- PDB-6j32: Crystal Structure Analysis of the Glycotransferase of kitacinnamycin -

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Basic information

Entry
Database: PDB / ID: 6j32
TitleCrystal Structure Analysis of the Glycotransferase of kitacinnamycin
ComponentsKcn28
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
Biological speciesKitasatospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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, 9items
OrganizationGrant numberCountry
National Science Foundation (China)81522042 China
National Science Foundation (China)21572100
National Science Foundation (China)81773591
National Science Foundation (China)81530089
National Science Foundation (China)81673333
National Science Foundation (China)81803380
National Science Foundation (China)21861142005
National Science Foundation (China)21761142001
National Science Foundation (China)21661140001
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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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


Theoretical massNumber of molelcules
Total (without water)174,4784
Polymers174,4784
Non-polymers00
Water3,009167
1
A: Kcn28
B: Kcn28
D: Kcn28


Theoretical massNumber of molelcules
Total (without water)130,8583
Polymers130,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Kcn28

C: Kcn28

C: Kcn28


Theoretical massNumber of molelcules
Total (without water)130,8583
Polymers130,8583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
Unit cell
Length a, b, c (Å)242.900, 242.900, 242.900
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 62 or resid 73...
21(chain B and (resid 2 through 62 or resid 73...
31(chain C and (resid 2 through 14 or (resid 15...
41(chain D and (resid 2 through 14 or (resid 15...

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 62 or resid 73...AA2 - 625 - 65
12ASPASPLYSLYS(chain A and (resid 2 through 62 or resid 73...AA73 - 13676 - 139
13PROPROPROPRO(chain A and (resid 2 through 62 or resid 73...AA2 - 3955 - 398
14PROPROPROPRO(chain A and (resid 2 through 62 or resid 73...AA2 - 3955 - 398
15PROPROPROPRO(chain A and (resid 2 through 62 or resid 73...AA2 - 3955 - 398
16PROPROPROPRO(chain A and (resid 2 through 62 or resid 73...AA2 - 3955 - 398
17PROPROPROPRO(chain A and (resid 2 through 62 or resid 73...AA2 - 3955 - 398
18PROPROPROPRO(chain A and (resid 2 through 62 or resid 73...AA2 - 3955 - 398
19PROPROPROPRO(chain A and (resid 2 through 62 or resid 73...AA2 - 3955 - 398
21PROPROPROPRO(chain B and (resid 2 through 62 or resid 73...BB2 - 625 - 65
22ASPASPLYSLYS(chain B and (resid 2 through 62 or resid 73...BB73 - 13676 - 139
23PROPROALAALA(chain B and (resid 2 through 62 or resid 73...BB2 - 3965 - 399
24PROPROALAALA(chain B and (resid 2 through 62 or resid 73...BB2 - 3965 - 399
25PROPROALAALA(chain B and (resid 2 through 62 or resid 73...BB2 - 3965 - 399
26PROPROALAALA(chain B and (resid 2 through 62 or resid 73...BB2 - 3965 - 399
27PROPROALAALA(chain B and (resid 2 through 62 or resid 73...BB2 - 3965 - 399
28PROPROALAALA(chain B and (resid 2 through 62 or resid 73...BB2 - 3965 - 399
29PROPROALAALA(chain B and (resid 2 through 62 or resid 73...BB2 - 3965 - 399
31PROPROSERSER(chain C and (resid 2 through 14 or (resid 15...CC2 - 145 - 17
32ARGARGARGARG(chain C and (resid 2 through 14 or (resid 15...CC1518
33PROPROPROPRO(chain C and (resid 2 through 14 or (resid 15...CC2 - 3955 - 398
34PROPROPROPRO(chain C and (resid 2 through 14 or (resid 15...CC2 - 3955 - 398
35PROPROPROPRO(chain C and (resid 2 through 14 or (resid 15...CC2 - 3955 - 398
36PROPROPROPRO(chain C and (resid 2 through 14 or (resid 15...CC2 - 3955 - 398
41PROPROSERSER(chain D and (resid 2 through 14 or (resid 15...DD2 - 145 - 17
42ARGARGARGARG(chain D and (resid 2 through 14 or (resid 15...DD1518
43PROPROPROPRO(chain D and (resid 2 through 14 or (resid 15...DD2 - 3955 - 398
44PROPROPROPRO(chain D and (resid 2 through 14 or (resid 15...DD2 - 3955 - 398
45PROPROPROPRO(chain D and (resid 2 through 14 or (resid 15...DD2 - 3955 - 398
46PROPROPROPRO(chain D and (resid 2 through 14 or (resid 15...DD2 - 3955 - 398

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Components

#1: Protein
Kcn28


Mass: 43619.430 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 64.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
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: BL17U1 / Wavelength: 0.97894 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.5→99.16 Å / Num. obs: 81520 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 59.28 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.038 / Rrim(I) all: 0.091 / Net I/σ(I): 10.7 / Num. measured all: 461803 / Scaling rejects: 3545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.5551.0272239644540.5450.5051.1491.699.9
12.99-99.165.50.03333896180.9970.0170.03725.798.1

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IYF

2iyf


Resolution: 2.5→70.119 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 4090 5.03 %
Rwork0.2688 77277 -
obs0.2696 81367 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.7 Å2 / Biso mean: 86.0655 Å2 / Biso min: 36.68 Å2
Refinement stepCycle: final / Resolution: 2.5→70.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11805 0 0 167 11972
Biso mean---60 -
Num. residues----1541
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7177X-RAY DIFFRACTION20.48TORSIONAL
12B7177X-RAY DIFFRACTION20.48TORSIONAL
13C7177X-RAY DIFFRACTION20.48TORSIONAL
14D7177X-RAY DIFFRACTION20.48TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.52940.35211260.358227022828100
2.5294-2.56030.37151280.358426362764100
2.5603-2.59270.34021330.346926372770100
2.5927-2.62680.38031020.355726892791100
2.6268-2.66280.37571480.344327282876100
2.6628-2.70080.36061250.336326512776100
2.7008-2.74110.38771630.366226072770100
2.7411-2.7840.40621460.352526792825100
2.784-2.82960.3621450.353326692814100
2.8296-2.87840.31231540.327126442798100
2.8784-2.93080.31591300.316526602790100
2.9308-2.98710.37831520.316526592811100
2.9871-3.04810.33581320.318626702802100
3.0481-3.11440.33671670.316226332800100
3.1144-3.18680.32051270.316227012828100
3.1868-3.26650.32831250.304626372762100
3.2665-3.35480.34211720.313226352807100
3.3548-3.45350.34191480.298226672815100
3.4535-3.5650.28661510.27612656280799
3.565-3.69240.26641400.26712556269696
3.6924-3.84030.25991370.27082655279299
3.8403-4.0150.25331200.242926862806100
4.015-4.22670.25221480.243326682816100
4.2267-4.49140.25231590.233226782837100
4.4914-4.83820.27661450.222126822827100
4.8382-5.32490.2241380.240327042842100
5.3249-6.0950.29741380.25852700283899
6.095-7.67760.25641390.2482614275396
7.6776-70.14680.22571520.21052774292699
Refinement TLS params.Method: refined / Origin x: -13.5493 Å / Origin y: 86.0425 Å / Origin z: -38.2027 Å
111213212223313233
T0.375 Å20.054 Å20.0182 Å2-0.425 Å20.0294 Å2--0.5121 Å2
L0.2988 °2-0.2299 °20.1995 °2-0.6121 °20.1331 °2--0.4312 °2
S0.0641 Å °0.0353 Å °-0.0755 Å °-0.0095 Å °0.0193 Å °-0.134 Å °0.1298 Å °0.0384 Å °-0.0732 Å °
Refinement TLS groupSelection details: all

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