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- PDB-4ecm: 2.3 Angstrom Crystal Structure of a Glucose-1-phosphate Thymidyly... -

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Basic information

Entry
Database: PDB / ID: 4ecm
Title2.3 Angstrom Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Bacillus anthracis in Complex with Thymidine-5-diphospho-alpha-D-glucose and Pyrophosphate
ComponentsGlucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE / Glucose-1-phosphate Thymidylyltransferase / 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
2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE / PYROPHOSPHATE 2- / glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMinasov, G. / Kuhn, M. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Structure of the Bacillus anthracis dTDP-L-rhamnose-biosynthetic enzyme glucose-1-phosphate thymidylyltransferase (RfbA).
Authors: Baumgartner, J. / Lee, J. / Halavaty, A.S. / Minasov, G. / Anderson, W.F. / Kuhn, M.L.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Atomic model
Revision 1.2Nov 15, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.name
Revision 1.3Sep 13, 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_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0193
Polymers30,2781
Non-polymers7402
Water4,071226
1
A: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,07412
Polymers121,1134
Non-polymers2,9618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Unit cell
Length a, b, c (Å)135.072, 135.072, 85.138
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A--4-

PHE

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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) / Gene: BA1228, BAS1135, BA_1228, 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: Chemical ChemComp-DAU / 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE


Mass: 564.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N2O16P2
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7.5 mg/mL, 0.5M NaCl, 0.01M Tris-HCl (pH 8.3), 0.001M Thymidine-5-diphospho-alpha-D-glucose. Screen: PACT (H8), 0.2 Sodium Sulfate, 0.1M TRIS propane, 20% (w/v) PEG 33500, VAPOR ...Details: Protein: 7.5 mg/mL, 0.5M NaCl, 0.01M Tris-HCl (pH 8.3), 0.001M Thymidine-5-diphospho-alpha-D-glucose. Screen: PACT (H8), 0.2 Sodium Sulfate, 0.1M TRIS propane, 20% (w/v) PEG 33500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 5, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 20938 / Num. obs: 20938 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 22.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1022 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HL3

3hl3


Resolution: 2.3→29.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.229 / SU ML: 0.094
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18588 1073 5.1 %RANDOM
Rwork0.15271 ---
all0.15442 19775 --
obs0.15442 19775 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.768 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 45 226 2211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222187
X-RAY DIFFRACTIONr_bond_other_d0.0010.021478
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9762983
X-RAY DIFFRACTIONr_angle_other_deg0.8533613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5565276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56724.216102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.42315379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9291514
X-RAY DIFFRACTIONr_chiral_restr0.1110.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02453
X-RAY DIFFRACTIONr_mcbond_it1.0441.51314
X-RAY DIFFRACTIONr_mcbond_other0.2851.5541
X-RAY DIFFRACTIONr_mcangle_it1.9322142
X-RAY DIFFRACTIONr_scbond_it3.0093873
X-RAY DIFFRACTIONr_scangle_it4.5514.5841
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 81 -
Rwork0.154 1416 -
obs-1416 100 %
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)
111.896326.30897.198477.426631.167216.44961.01230.3263-0.195-0.5147-1.4531-0.1708-1.2656-1.77150.44080.50280.1628-0.02960.5828-0.29610.677367.7583-16.36490.3832
20.2385-0.2210.81490.9586-1.32923.2388-0.0034-0.0594-0.0113-0.03350.14660.1218-0.0222-0.2785-0.14320.09220.0215-0.00490.03260.01050.099360.6445-13.165529.9024
30.38680.14410.09340.7168-0.1640.77590.0117-0.00410.009-0.0389-0.0060.0389-0.00250.0543-0.00570.08450.01580.00130.0080.00270.053967.4003-13.025724.0596
40.5740.12570.25622.8831-0.46060.670.01210.0122-0.0434-0.02880.00560.13860.0703-0.1378-0.01770.095-0.0304-0.02420.0476-0.0130.053852.9618-28.565619.4155
52.73721.0588-0.1663.8413-0.92041.8757-0.0674-0.19840.32710.04340.06380.6212-0.2415-0.32350.00360.1240.0247-0.03340.0894-0.01090.154950.4555-13.570314.2576
60.8644-0.05890.5990.7816-0.01761.27550.0084-0.0114-0.015-0.02410.0133-0.09860.209-0.0031-0.02170.06920.00240.0050.002-0.00950.064968.2182-25.679429.428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4
2X-RAY DIFFRACTION2A0 - 16
3X-RAY DIFFRACTION3A17 - 130
4X-RAY DIFFRACTION4A131 - 175
5X-RAY DIFFRACTION5A176 - 206
6X-RAY DIFFRACTION6A207 - 243

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