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- PDB-3hl3: 2.76 Angstrom Crystal Structure of a Putative Glucose-1-Phosphate... -

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Basic information

Entry
Database: PDB / ID: 3hl3
Title2.76 Angstrom Crystal Structure of a Putative Glucose-1-Phosphate Thymidylyltransferase from Bacillus anthracis in Complex with a Sucrose.
ComponentsGlucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE / Glucose-1-phosphate thymidylyltransferase / idp01254 / sucrose / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / extracellular polysaccharide biosynthetic process
Similarity search - Function
Glucose-1-phosphate thymidylyltransferase, short form / Nucleotidyl transferase domain / Nucleotidyl transferase / 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
sucrose / glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsMinasov, G. / Shuvalova, L. / Halavaty, A. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.76 Angstrom Crystal Structure of a Putative Glucose-1-Phosphate Thymidylyltransferase from Bacillus anthracis in Complex with a Sucrose.
Authors: Minasov, G. / Shuvalova, L. / Halavaty, A. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6212
Polymers30,2781
Non-polymers3421
Water66737
1
A: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2414
Polymers60,5572
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+11
Buried area3420 Å2
ΔGint-6 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.425, 134.425, 85.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

#1: Protein Glucose-1-phosphate thymidylyltransferase


Mass: 30278.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA1228, BAS1135, BA_1228, GBAA1228, GBAA_1228 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3
References: UniProt: Q81TP2, UniProt: A0A6L8PCC3*PLUS, glucose-1-phosphate thymidylyltransferase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein Solution: 7.6 mg/mL, 0.25M NaCl, 0.01M Tris-HCl, pH 8.3. Screen: Classics II, drop B10, 0.8M Succinic acid, pH 7.0 Freezing solution: 25% Sucrose, 0.4M Succinic acid, pH 7.0., VAPOR ...Details: Protein Solution: 7.6 mg/mL, 0.25M NaCl, 0.01M Tris-HCl, pH 8.3. Screen: Classics II, drop B10, 0.8M Succinic acid, pH 7.0 Freezing solution: 25% Sucrose, 0.4M Succinic acid, pH 7.0., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 12153 / Num. obs: 12153 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 71.8 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 4.9 / Num. unique all: 601 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MC3

1mc3


Resolution: 2.76→29.1 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 19.171 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Isotropic Individual Temperature Factor Refinement
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.379 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20573 580 4.8 %RANDOM
Rwork0.17302 ---
all0.17457 11573 --
obs0.17457 11573 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.525 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å2-0 Å2
2--0.32 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.76→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 23 37 2003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222062
X-RAY DIFFRACTIONr_bond_other_d0.0010.021411
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9722796
X-RAY DIFFRACTIONr_angle_other_deg0.76533443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.845256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91824.31695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32615361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4681512
X-RAY DIFFRACTIONr_chiral_restr0.0740.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
X-RAY DIFFRACTIONr_mcbond_it0.8211.51249
X-RAY DIFFRACTIONr_mcbond_other0.1731.5519
X-RAY DIFFRACTIONr_mcangle_it1.64722020
X-RAY DIFFRACTIONr_scbond_it2.7533813
X-RAY DIFFRACTIONr_scangle_it4.4764.5776
LS refinement shellResolution: 2.76→2.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 44 -
Rwork0.248 807 -
obs-807 97.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.06240.52011.56552.3018-1.7439.61360.2750.052-0.18750.1968-0.07320.17110.1223-0.2368-0.20180.07870.0587-0.00760.1221-0.0260.145145.865749.023833.0391
24.5298-0.6823-0.47311.65772.28357.2846-0.08260.1403-0.26930.1123-0.06030.27490.2356-0.18220.14280.08920.0902-0.00190.1610.02960.172739.224553.862623.8934
32.8881-1.6310.37553.6693-0.78862.81620.08080.2771-0.4154-0.1103-0.15130.19320.32240.02640.07040.09140.0899-0.01610.1953-0.10410.126149.988137.560817.1749
44.67370.31862.06135.0126-0.41855.12720.20240.2486-0.327-0.1380.04850.82370.4777-0.5386-0.25090.22120.1087-0.05240.2638-0.05150.262641.363737.336915.0366
59.77151.42211.195210.4033-4.30827.3394-0.11080.21350.05910.78240.0409-0.7504-0.04580.46330.06990.1050.0555-0.06770.1661-0.04350.088155.526250.10334.8754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 41
2X-RAY DIFFRACTION2A42 - 103
3X-RAY DIFFRACTION3A104 - 181
4X-RAY DIFFRACTION4A182 - 217
5X-RAY DIFFRACTION5A218 - 245

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