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- PDB-3pkq: Q83D Variant of S. Enterica RmlA with dGTP -

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Basic information

Entry
Database: PDB / ID: 3pkq
TitleQ83D Variant of S. Enterica RmlA with dGTP
ComponentsGlucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE / nucleotidylyltransferase / Directed evolution / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process / polysaccharide biosynthetic process / magnesium ion binding
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'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsChang, A. / Moretti, R. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution.
Authors: Moretti, R. / Chang, A. / Peltier-Pain, P. / Bingman, C.A. / Phillips, G.N. / Thorson, J.S.
History
DepositionNov 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Glucose-1-phosphate thymidylyltransferase
C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,36116
Polymers129,8934
Non-polymers2,46912
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2469
Polymers64,9462
Non-polymers1,3007
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-32 kcal/mol
Surface area23600 Å2
MethodPISA
3
C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1167
Polymers64,9462
Non-polymers1,1695
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-27 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.400, 109.400, 110.075
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGchain CCC4 - 2904 - 290
2THRTHRchain AAA3 - 2903 - 290
3METMETchain BBB1 - 2901 - 290
4ARGARGchain DDD4 - 2904 - 290

NCS oper:
IDCodeMatrixVector
1given(-0.995791, 0.044507, 0.080116), (0.033591, -0.636087, 0.770886), (0.08527, 0.770333, 0.631915)-32.812302, 80.747299, -36.218601
2given(-0.966824, 0.238779, -0.09075), (0.220087, 0.598332, -0.770429), (-0.129664, -0.764842, -0.631034)-41.773701, 23.058201, 35.4035
3given(0.9708, -0.235614, 0.045086), (-0.234788, -0.971777, -0.022895), (0.049208, 0.011641, -0.998721)11.1874, 92.732101, 0.265284

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Components

#1: Protein
Glucose-1-phosphate thymidylyltransferase / dTDP-glucose pyrophosphorylase / Ep / dTDP-glucose synthase


Mass: 32473.209 Da / Num. of mol.: 4 / Fragment: Q83D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: rfbA, rmlA, STM2095 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P26393, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (15 mg/ml RmlA Q83s protein, 10mM MOPS pH 7.5, 25mM dGTP) mixed in a 1:1 ratio with the well solution (10% MEPEG5K, 120mM MgCl2, 100mM Tris pH 8.5, 1mM Suramine) ...Details: Protein Solution (15 mg/ml RmlA Q83s protein, 10mM MOPS pH 7.5, 25mM dGTP) mixed in a 1:1 ratio with the well solution (10% MEPEG5K, 120mM MgCl2, 100mM Tris pH 8.5, 1mM Suramine) Cryoprotected with 20% Ethylene Glycol, 10% MEPEG5K, 120mM MgCl2, 100mM Tris pH 8.5, 1mM Suramine, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2009 / Details: mirrors and beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 49418 / % possible obs: 97.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 43.13 Å2 / Rmerge(I) obs: 0.085 / Χ2: 1.034 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.442.90.52618190.98272.3
2.44-2.493.40.50721180.93783.9
2.49-2.533.90.47323690.97293.3
2.53-2.594.60.44324930.9698.7
2.59-2.645.10.424950.97799.5
2.64-2.75.50.38925000.99399.8
2.7-2.775.90.32625650.99100
2.77-2.8560.29325011.025100
2.85-2.936.10.24625371.089100
2.93-3.026.10.21625381.091100
3.02-3.136.10.17625331.044100
3.13-3.266.10.14425251.048100
3.26-3.416.10.1125461.004100
3.41-3.586.10.08525231.012100
3.58-3.816.10.06825321.018100
3.81-4.16.10.06825491.081100
4.1-4.526.10.06525461.257100
4.52-5.1760.05125621.005100
5.17-6.5160.04725581.011100
6.51-505.80.03526091.01299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.66 Å44.71 Å
Translation2.66 Å44.71 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MP4

1mp4


Resolution: 2.4→44.708 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.36 / σ(F): 1.35 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 2516 5.1 %
Rwork0.2119 --
obs0.2148 49377 97.37 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.746 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 185.56 Å2 / Biso mean: 57.2362 Å2 / Biso min: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8861 0 150 225 9236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099236
X-RAY DIFFRACTIONf_angle_d1.18112518
X-RAY DIFFRACTIONf_chiral_restr0.0981374
X-RAY DIFFRACTIONf_plane_restr0.0051592
X-RAY DIFFRACTIONf_dihedral_angle_d15.2253459
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2210X-RAY DIFFRACTIONPOSITIONAL0.41
12A2210X-RAY DIFFRACTIONPOSITIONAL0.41
13B2201X-RAY DIFFRACTIONPOSITIONAL0.188
14D2203X-RAY DIFFRACTIONPOSITIONAL0.092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3999-2.4460.3339930.29611951204473
2.446-2.49590.38841300.27182281241186
2.4959-2.55020.33271400.25892537267795
2.5502-2.60950.31721320.25182648278099
2.6095-2.67480.33051440.23926532797100
2.6748-2.74710.31021440.236726552799100
2.7471-2.82790.27061410.229426622803100
2.8279-2.91920.30071580.23526542812100
2.9192-3.02350.32321280.233326722800100
3.0235-3.14450.30811560.23126362792100
3.1445-3.28760.28881520.22926672819100
3.2876-3.46080.28441380.226626962834100
3.4608-3.67760.28791310.217226802811100
3.6776-3.96140.2531560.209426652821100
3.9614-4.35970.23841250.185126802805100
4.3597-4.98990.24081460.173827202866100
4.9899-6.28390.23331660.209226562822100
6.2839-44.71570.23071360.186127482884100

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