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- PDB-1qgs: UDP-MAGNESIUM COMPLEX OF SPSA FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1qgs
TitleUDP-MAGNESIUM COMPLEX OF SPSA FROM BACILLUS SUBTILIS
ComponentsPROTEIN (SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA)
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


glycosyltransferase activity
Similarity search - Function
: / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Spore coat polysaccharide biosynthesis protein SpsA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCharnock, S.J.
CitationJournal: Biochemistry / Year: 1999
Title: Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms.
Authors: Charnock, S.J. / Davies, G.J.
History
DepositionMay 4, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6365
Polymers30,0911
Non-polymers5454
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.420, 141.997, 81.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA)


Mass: 30090.936 Da / Num. of mol.: 1 / Fragment: WHOLE MOLECULE
Source method: isolated from a genetically manipulated source
Details: GLYCEROL MAGNESIUM UDP / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SPSA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL 21 / References: UniProt: P39621
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39 % / Description: ISOMORPHOUS WITH NATIVE
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Charnock, S.J., (1999) Acta Crystallogr., D55, 677.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
2100 mMHEPES1drop
3200 mM1dropMgCl2
415 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 18368 / % possible obs: 96 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 18.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.32 / % possible all: 90
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QG8

1qg8


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 916 5 %RANDOM
Rwork0.19 ---
obs-18262 96 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 33 191 2192
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0320.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.654
X-RAY DIFFRACTIONp_mcangle_it2.56
X-RAY DIFFRACTIONp_scbond_it1.94
X-RAY DIFFRACTIONp_scangle_it3.16
X-RAY DIFFRACTIONp_plane_restr0.010.04
X-RAY DIFFRACTIONp_chiral_restr0.1250.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor14.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_mcbond_it1.654
X-RAY DIFFRACTIONp_scbond_it1.94
X-RAY DIFFRACTIONp_mcangle_it2.56
X-RAY DIFFRACTIONp_scangle_it3.16

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