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- PDB-1qgq: UDP-MANGANESE COMPLEX OF SPSA FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1qgq
TitleUDP-MANGANESE 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 / MIR / Resolution: 1.5 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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.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

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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)30,6665
Polymers30,0911
Non-polymers5754
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.330, 142.360, 81.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 MANGANESE 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

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Non-polymers , 5 types, 299 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


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


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


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.04 Å3/Da / Density % sol: 39 %
Crystal growpH: 8 / Details: 15% PEG 8000, 100MM HEPES BUFFER 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: PX9.6 / Wavelength: 0.87
DetectorType: ADSC / Detector: CCD / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→25.8 Å / Num. obs: 43230 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 22.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.27 / % possible all: 86
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 18 Å / % possible obs: 99 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 1.81 Å / % possible obs: 100 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2141 5 %RANDOM
Rwork0.16 ---
obs-42563 96 %-
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 33 295 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.44
X-RAY DIFFRACTIONp_mcangle_it3.96
X-RAY DIFFRACTIONp_scbond_it4.44
X-RAY DIFFRACTIONp_scangle_it5.76
X-RAY DIFFRACTIONp_plane_restr0.01370.04
X-RAY DIFFRACTIONp_chiral_restr0.1480.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2580.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.97
X-RAY DIFFRACTIONp_staggered_tor1415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.75 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.028
X-RAY DIFFRACTIONp_mcbond_it3.44
X-RAY DIFFRACTIONp_scbond_it4.44
X-RAY DIFFRACTIONp_mcangle_it3.96
X-RAY DIFFRACTIONp_scangle_it5.76

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