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- PDB-4fzr: Crystal Structure of SsfS6, Streptomyces sp. SF2575 glycosyltrans... -

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Basic information

Entry
Database: PDB / ID: 4fzr
TitleCrystal Structure of SsfS6, Streptomyces sp. SF2575 glycosyltransferase
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
Biological speciesStreptomyces sp. SF2575 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.397 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 7, 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
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SsfS6


Theoretical massNumber of molelcules
Total (without water)43,2251
Polymers43,2251
Non-polymers00
Water1,982110
1
A: SsfS6

A: SsfS6


Theoretical massNumber of molelcules
Total (without water)86,4502
Polymers86,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area3100 Å2
ΔGint-12 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.605, 82.605, 230.516
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein SsfS6


Mass: 43225.000 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 %
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 (1.13~1.40 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 (1.13~1.40 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

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 21-ID-D11.12715
SYNCHROTRONAPS 21-ID-G20.97856
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDJun 2, 2012
MARMOSAIC 300 mm CCD2CCDMar 31, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1KohzuSINGLE WAVELENGTHMx-ray1
2Diamond [111]SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.127151
20.978561
ReflectionResolution: 2.4→50 Å / Num. all: 19209 / Num. obs: 19017 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 70.76 Å2 / Rmerge(I) obs: 0.094 / Χ2: 0.923 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible all
2.4-2.4410.18580.8011,292.2
2.44-2.4911.99320.8211,2100
2.49-2.53129170.8471,2100
2.53-2.5911.89530.8541,2100
2.59-2.64129150.8971,2100
2.64-2.711.99370.9191,2100
2.7-2.7711.89500.9851,2100
2.77-2.85129401.0361,2100
2.85-2.9311.99311.1031,2100
2.93-3.0211.99421.1121,2100
3.02-3.1311.89441.1191,2100
3.13-3.2611.89511.1041,2100
3.26-3.4111.89501.0121,2100
3.41-3.5811.69700.9431,2100
3.58-3.8111.59540.9071,2100
3.81-4.111.49670.9291,2100
4.1-4.5211.29830.8361,299.9
4.52-5.1711.110010.7471,2100
5.17-6.5111.110140.7781,2100
6.51-508.910080.6021,288.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1063refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXPHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.397→30.763 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.7525 / SU ML: 0.32 / σ(F): 1.34 / Phase error: 29.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2617 979 5.18 %RANDOM, ASSIGN TEST SET IN THIN RESOLUTION SHELLS
Rwork0.2241 ---
obs0.226 18899 98.81 %-
all-19126 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.15 Å2 / Biso mean: 39.7201 Å2 / Biso min: 6.7 Å2
Refinement stepCycle: LAST / Resolution: 2.397→30.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2620 0 0 110 2730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042700
X-RAY DIFFRACTIONf_angle_d0.8613686
X-RAY DIFFRACTIONf_chiral_restr0.044433
X-RAY DIFFRACTIONf_plane_restr0.004478
X-RAY DIFFRACTIONf_dihedral_angle_d14.0081003
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3975-2.52380.34141310.30372411254296
2.5238-2.68180.35031730.279424862659100
2.6818-2.88880.2722970.263325772674100
2.8888-3.17920.34031470.241725552702100
3.1792-3.63860.2831470.212925612708100
3.6386-4.58180.19941470.194926242771100
4.5818-30.76550.26271370.22742706284396

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