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- PDB-4g2t: Crystal Structure of Streptomyces sp. SF2575 glycosyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 4g2t
TitleCrystal Structure of Streptomyces sp. SF2575 glycosyltransferase SsfS6, complexed with thymidine diphosphate
ComponentsSsfS6
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NATPRO / Glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process
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-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-DIPHOSPHATE / SsfS6
Similarity search - Component
Biological speciesStreptomyces sp. SF2575 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.405 Å
AuthorsWang, F. / Zhou, M. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)
CitationJournal: Proteins / Year: 2013
Title: Crystal structure of SsfS6, the putative C-glycosyltransferase involved in SF2575 biosynthesis.
Authors: Wang, F. / Zhou, M. / Singh, S. / Yennamalli, R.M. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N.
History
DepositionJul 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Derived calculations
Revision 1.2May 1, 2013Group: Database references
Revision 1.3Jul 3, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SsfS6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4892
Polymers43,0871
Non-polymers4021
Water1,20767
1
A: SsfS6
hetero molecules

A: SsfS6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9784
Polymers86,1742
Non-polymers8042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area4700 Å2
ΔGint-40 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.141, 81.141, 229.906
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-537-

HOH

21A-558-

HOH

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Components

#1: Protein SsfS6


Mass: 43086.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. SF2575 (bacteria) / Gene: ssfS6 / Production host: Escherichia coli (E. coli) / References: UniProt: D6MSX4
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: Protein Solution (11.4 mg/ml SsfS6 protein, 50mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.13~1.26 M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, ...Details: Protein Solution (11.4 mg/ml SsfS6 protein, 50mM Tris pH 8.0) mixed in a 1:1 ratio with the well solution (1.13~1.26 M Sodium phosphate monobasic monohydrate / Potassium phosphate dibasic, pH 8.2) Cryoprotected with 100% Paratone-N, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12715 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2012
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12715 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 18241 / Num. obs: 18150 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Rmerge(I) obs: 0.2 / Χ2: 1.027 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible all
2.4-2.4414.28870.811100
2.44-2.4915.28740.8361100
2.49-2.5315.88890.8621100
2.53-2.5916.68830.8951100
2.59-2.6417.18780.9041100
2.64-2.717.19070.9471100
2.7-2.7717.78821.04199.9
2.77-2.8517.48761.0791100
2.85-2.9317.38951.1541100
2.93-3.0217.48851.1611100
3.02-3.13179031.2481100
3.13-3.2616.99031.232199.8
3.26-3.41169001.247199.9
3.41-3.5815.89021.137199.3
3.58-3.8115.49171.118199.7
3.81-4.115.29131.085199.3
4.1-4.5215.19350.974199.9
4.52-5.1714.99380.875199.9
5.17-6.5115.39650.83199.9
6.51-5011.910181.027193.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1063refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHENIXPHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FZR

4fzr


Resolution: 2.405→44.49 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.7096 / SU ML: 0.35 / σ(F): 1.36 / Phase error: 33.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 897 4.97 %RANDOM, ASSIGN TEST SET IN THIN RESOLUTION SHELLS
Rwork0.2441 ---
obs0.2454 18057 98.83 %-
all-18271 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.61 Å2 / Biso mean: 32.2766 Å2 / Biso min: 3.64 Å2
Refinement stepCycle: LAST / Resolution: 2.405→44.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 25 67 2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032771
X-RAY DIFFRACTIONf_angle_d0.7583787
X-RAY DIFFRACTIONf_chiral_restr0.049444
X-RAY DIFFRACTIONf_plane_restr0.004487
X-RAY DIFFRACTIONf_dihedral_angle_d13.81024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4054-2.5560.38721320.32492723285596
2.556-2.75340.33641650.290327742939100
2.7534-3.03040.28261250.275828552980100
3.0304-3.46880.30331470.249428593006100
3.4688-4.36970.25771650.220128943059100
4.3697-44.49730.24321630.23553055321898

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