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

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Basic information

Entry
Database: PDB / ID: 4amb
TitleCrystal structure of the glycosyltransferase SnogD from Streptomyces nogalater
ComponentsSNOGD
KeywordsTRANSFERASE / 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: 2.62 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 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 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_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_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: SNOGD
B: SNOGD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2813
Polymers83,8932
Non-polymers3881
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-19.5 kcal/mol
Surface area30850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.911, 170.955, 69.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8528, -0.5222, -0.002406), (-0.5222, 0.8528, -0.003275), (0.003762, -0.001537, -1)
Vector: -43.56, -12.34, -14.85)

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Components

#1: Protein SNOGD


Mass: 41946.566 Da / Num. of mol.: 2 / Fragment: RESIDUES 13-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES NOGALATER (bacteria) / Plasmid: PNIC-BSAI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RN61
#2: Chemical ChemComp-DUD / DEOXYURIDINE-5'-DIPHOSPHATE


Mass: 388.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.3 Å3/Da / Density % sol: 46.5 % / Description: NONE
Crystal growpH: 5.2 / Details: 26% (W/V) PEG 3350, 0.1 M CITRATE PH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.62→60 Å / Num. obs: 23310 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.9
Reflection shellResolution: 2.62→2.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 86.7

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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 3D0Q

3d0q


Resolution: 2.62→50 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.83 / SU B: 14.565 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29691 1207 5.2 %RANDOM
Rwork0.22313 ---
obs0.22689 22091 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.945 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å20 Å2
2--1.77 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.62→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5434 0 24 115 5573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195594
X-RAY DIFFRACTIONr_bond_other_d0.0040.023769
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9977642
X-RAY DIFFRACTIONr_angle_other_deg2.11939187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0945742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03522.427206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55115830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.221552
X-RAY DIFFRACTIONr_chiral_restr0.0710.2885
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216301
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021099
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
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 74 -
Rwork0.312 1276 -
obs--80.07 %

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