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- PDB-4an4: Crystal structure of the glycosyltransferase SnogD from Streptomy... -

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Basic information

Entry
Database: PDB / ID: 4an4
TitleCrystal structure of the glycosyltransferase SnogD from Streptomyces nogalater
ComponentsGLYCOSYL TRANSFERASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / POLYKETIDE BIOSYNTHESIS / GT1 FAMILY / NOGALAMYCIN
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / identical protein binding
Similarity search - Function
: / Erythromycin biosynthesis protein CIII-like, N-terminal domain / Erythromycin biosynthesis protein CIII-like, central / : / Erythromycin biosynthesis protein CIII-like, C-terminal domain / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DEOXYURIDINE-5'-DIPHOSPHATE / Putative glycosyl transferase
Similarity search - Component
Biological speciesSTREPTOMYCES NOGALATER (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsClaesson, M. / Siitonen, V. / Dobritzsch, D. / Metsa-Ketela, M. / Schneider, G.
CitationJournal: FEBS J. / Year: 2012
Title: Crystal Structure of the Glycosyltransferase Snogd from the Biosynthetic Pathway of the Nogalamycin in Streptomyces Nogalater.
Authors: Claesson, M. / Siitonen, V. / Dobritzsch, D. / Metsa-Ketela, M. / Schneider, G.
History
DepositionMar 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCOSYL TRANSFERASE
B: GLYCOSYL TRANSFERASE
C: GLYCOSYL TRANSFERASE
D: GLYCOSYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,6716
Polymers167,8944
Non-polymers7762
Water86548
1
A: GLYCOSYL TRANSFERASE
B: GLYCOSYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3353
Polymers83,9472
Non-polymers3881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-17.9 kcal/mol
Surface area29570 Å2
MethodPISA
2
C: GLYCOSYL TRANSFERASE
D: GLYCOSYL TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3353
Polymers83,9472
Non-polymers3881
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-19.8 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.641, 70.078, 176.031
Angle α, β, γ (deg.)90.00, 91.71, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLYAA11 - 39021 - 400
21GLNGLNGLYGLYBB11 - 39021 - 400
12GLNGLNALAALAAA11 - 38921 - 399
22GLNGLNALAALACC11 - 38921 - 399
13SERSERGLYGLYAA12 - 39022 - 400
23SERSERGLYGLYDD12 - 39022 - 400
14GLNGLNALAALABB11 - 38921 - 399
24GLNGLNALAALACC11 - 38921 - 399
15SERSERGLYGLYBB12 - 39022 - 400
25SERSERGLYGLYDD12 - 39022 - 400
16SERSERALAALACC12 - 38922 - 399
26SERSERALAALADD12 - 38922 - 399

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.8659, -0.0105, -0.5002), (0.01135, -0.9999, 0.001347), (-0.5001, -0.004509, 0.8659)-14.16, 56.04, -3.898
2given(0.9224, 0.02019, 0.3856), (0.02742, -0.9995, -0.01324), (0.3852, 0.02279, -0.9226)17.24, 80.66, -86.67
3given(-0.9887, -0.02023, -0.1484), (-0.01852, 0.9997, -0.01289), (0.1486, -0.009994, -0.9888)3.422, 24.59, -87.56

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Components

#1: Protein
GLYCOSYL TRANSFERASE / SNOGD


Mass: 41973.613 Da / Num. of mol.: 4 / Fragment: RESIDUES 13-390
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS SUBJECTED TO METHYLATION. MOST LYSINE RESIDUES AND THE N-TERMINAL AMINO GROUP SHOULD BE DIMETHYLATED. ONLY FOR K384 DIMETHYLATION WAS VISIBLE IN THE ELECTRON DENSITY MAP AND THUS MODELED.
Source: (gene. exp.) STREPTOMYCES NOGALATER (bacteria) / Plasmid: PNIC-BSAI / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: Q9RN61
#2: Chemical ChemComp-DUD / DEOXYURIDINE-5'-DIPHOSPHATE


Mass: 388.162 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDEOXYURIDINE-5'-DIPHOSPHATE (DUD): POSITION OF DIPHOSPHATE MOIETY NOT WELL FIXED - DOUBLE ...DEOXYURIDINE-5'-DIPHOSPHATE (DUD): POSITION OF DIPHOSPHATE MOIETY NOT WELL FIXED - DOUBLE CONFORMATION POSSIBLE
Sequence detailsN-TERMINAL HIS-TAG

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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: 2.37 Å3/Da / Density % sol: 48.18 % / Description: NONE
Crystal growpH: 6.8
Details: 15 % (W/V) PEG 8000 0.16 M CALCIUM ACETATE 0.08 M SODIUM CACODYLATE PH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.7→58.6 Å / Num. obs: 42845 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.2 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AMB

4amb


Resolution: 2.7→60 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.681 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. SEVERAL LOOPS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.26595 2158 5 %RANDOM
Rwork0.22746 ---
obs0.22947 40687 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.817 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å2-0.01 Å2
2--0.9 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.7→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10218 0 48 48 10314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910492
X-RAY DIFFRACTIONr_bond_other_d0.0060.027045
X-RAY DIFFRACTIONr_angle_refined_deg1.428214331
X-RAY DIFFRACTIONr_angle_other_deg1.718317163
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.94251377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80222.35383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.695151539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.531599
X-RAY DIFFRACTIONr_chiral_restr0.0680.21685
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111713
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022046
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A112220.14
12B112220.14
21A101750.16
22C101750.16
31A107920.15
32D107920.15
41B101110.16
42C101110.16
51B110810.15
52D110810.15
61C98770.17
62D98770.17
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 129 -
Rwork0.405 2585 -
obs--88.2 %

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