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- PDB-1h7l: dTDP-MAGNESIUM COMPLEX OF SPSA FROM BACILLUS SUBTILIS -

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Basic information

Entry
Database: PDB / ID: 1h7l
TitledTDP-MAGNESIUM COMPLEX OF SPSA FROM BACILLUS SUBTILIS
ComponentsSPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


: / 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
THYMIDINE-5'-DIPHOSPHATE / Spore coat polysaccharide biosynthesis protein SpsA
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsTarbouriech, N. / Charnock, S.J. / Davies, G.J.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Three-Dimensional Structures of the Mn and Mg Dtdp Complexes of the Family Gt-2 Glycosyltransferase Spsa: A Comparison with Related Ndp-Sugar Glycosyltransferases.
Authors: Tarbouriech, N. / Charnock, S.J. / Davies, G.J.
History
DepositionJul 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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 / _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 / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,5424
Polymers30,0911
Non-polymers4513
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.320, 142.310, 81.310
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-2027-

HOH

21A-2090-

HOH

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Components

#1: Protein SPORE COAT POLYSACCHARIDE BIOSYNTHESIS PROTEIN SPSA


Mass: 30090.936 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GLYCEROL MAGNESIUM DTDP / Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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-TYD / THYMIDINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL METHIONINE CLEAVED POST-TRANSLATIONALLY

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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
pH: 8 / 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: ESRF / Beamline: ID14-4 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→18 Å / Num. obs: 43230 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.2
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 18 Å / % possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGQ

1qgq


Resolution: 1.98→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.306 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 995 5.1 %RANDOM
Rwork0.192 ---
obs0.194 18438 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 27 126 2129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222053
X-RAY DIFFRACTIONr_bond_other_d0.0010.021797
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.611.9582781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.50534192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022240
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02437
X-RAY DIFFRACTIONr_nbd_refined0.2470.3423
X-RAY DIFFRACTIONr_nbd_other0.2270.31803
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.5105
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.17402
X-RAY DIFFRACTIONr_metal_ion_refined0.14501
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1770.313
X-RAY DIFFRACTIONr_symmetry_hbond_refined1.4390.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9621.51196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84321948
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6713857
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5164.5833
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: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 78
Rwork0.218 1260
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.2283
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.02 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Num. reflection Rfree: 78 / Rfactor obs: 0.218

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