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- PDB-3pkp: Q83S Variant of S. Enterica RmlA with dATP -

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Basic information

Entry
Database: PDB / ID: 3pkp
TitleQ83S Variant of S. Enterica RmlA with dATP
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 / extracellular 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'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.3Feb 21, 2024Group: 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_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_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_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
I: Glucose-1-phosphate thymidylyltransferase
J: Glucose-1-phosphate thymidylyltransferase
K: Glucose-1-phosphate thymidylyltransferase
L: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,88032
Polymers259,5628
Non-polymers4,31824
Water3,063170
1
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)131,94016
Polymers129,7814
Non-polymers2,15912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: Glucose-1-phosphate thymidylyltransferase
J: Glucose-1-phosphate thymidylyltransferase
K: Glucose-1-phosphate thymidylyltransferase
L: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,94016
Polymers129,7814
Non-polymers2,15912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9708
Polymers64,8902
Non-polymers1,0806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-52 kcal/mol
Surface area24540 Å2
MethodPISA
4
C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9708
Polymers64,8902
Non-polymers1,0806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-52 kcal/mol
Surface area23480 Å2
MethodPISA
5
I: Glucose-1-phosphate thymidylyltransferase
J: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9708
Polymers64,8902
Non-polymers1,0806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-52 kcal/mol
Surface area24330 Å2
MethodPISA
6
K: Glucose-1-phosphate thymidylyltransferase
L: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9708
Polymers64,8902
Non-polymers1,0806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-50 kcal/mol
Surface area24010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.879, 134.313, 175.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51I
61J
71K
81L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 3 - 290 / Label seq-ID: 3 - 290

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 3:290 )AA
2chain B and (resseq 3:290 )BB
3chain C and (resseq 3:290 )CC
4chain D and (resseq 3:290 )DD
5chain I and (resseq 3:290 )IE
6chain J and (resseq 3:290 )JF
7chain K and (resseq 3:290 )KG
8chain L and (resseq 3:290 )LH

NCS oper:
IDCodeMatrixVector
1given(-0.998974, 0.032145, -0.031912), (0.028684, -0.096322, -0.994937), (-0.035056, -0.994831, 0.095301)81.144302, -38.210602, -32.1852
2given(-0.65407, -0.566247, -0.501555), (-0.571997, -0.063641, 0.817783), (-0.494987, 0.821775, -0.282266)48.964699, 40.122299, -11.7157
3given(0.643408, 0.532437, 0.550034), (0.532948, -0.827333, 0.177444), (0.549539, 0.178971, -0.816074)34.668301, -29.3097, -75.052002
4given(0.999883, 0.011645, 0.009888), (-0.010083, 0.016741, 0.999809), (0.011477, -0.999792, 0.016857)-27.2609, -32.664101, -34.758301
5given(-0.999691, 0.020727, 0.013721), (0.019012, 0.993172, -0.115097), (-0.016013, -0.114801, -0.993259)108.560997, -1.32881, -2.59388
6given(-0.660074, 0.511877, -0.549804), (-0.570778, -0.817586, -0.075932), (-0.48838, 0.263695, 0.831835)102.307999, 30.5916, -17.3386
7given(0.669232, -0.532799, 0.517932), (0.516568, -0.167439, -0.839715), (0.534121, 0.829512, 0.163171)-20.2384, -20.5341, -66.739403

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Components

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


Mass: 32445.201 Da / Num. of mol.: 8 / Mutation: E83S
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-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (12 mg/ml RmlA Q83S protein, 10mM MOPS pH 7.5, 25mM dATP) mixed in a 1:1 ratio with the well solution (20% MEPEG5K, 120mM MgCl2, 100mM Tris pH 8.5, 1mM Suramine) ...Details: Protein Solution (12 mg/ml RmlA Q83S protein, 10mM MOPS pH 7.5, 25mM dATP) mixed in a 1:1 ratio with the well solution (20% MEPEG5K, 120mM MgCl2, 100mM Tris pH 8.5, 1mM Suramine) Cryoprotected with 20% Ethylene Glycol, 20% 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: 2.6→50 Å / Num. obs: 77557 / % possible obs: 96.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 50.64 Å2 / Rmerge(I) obs: 0.08 / Χ2: 1.01 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.644.90.58831470.91979.5
2.64-2.695.20.61933051.03482.4
2.69-2.745.60.54934060.95485.3
2.74-2.85.90.48734910.97187.9
2.8-2.866.30.46636830.9793.1
2.86-2.936.50.43538510.99297
2.93-36.80.40239950.99799.7
3-3.087.10.31939741.04699.9
3.08-3.177.20.28239901.055100
3.17-3.287.30.21140081.091100
3.28-3.397.40.16340151.083100
3.39-3.537.50.13640151.14100
3.53-3.697.50.10740050.985100
3.69-3.887.50.08140120.943100
3.88-4.137.50.07740411.023100
4.13-4.457.50.06240540.996100
4.45-4.897.50.04640471.015100
4.89-5.67.40.04241101.023100
5.6-7.057.40.03841180.967100
7.05-506.90.02842900.9199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.89 Å43.39 Å
Translation2.89 Å43.39 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 / Resolution: 2.6→43.387 Å / Occupancy max: 1 / Occupancy min: 0.8 / SU ML: 0.37 / σ(F): 0 / Phase error: 30.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 1889 2.59 %
Rwork0.1997 --
obs0.2013 72817 90.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.455 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 235.95 Å2 / Biso mean: 83.0882 Å2 / Biso min: 11.76 Å2
Baniso -1Baniso -2Baniso -3
1--7.7525 Å20 Å2-0 Å2
2--11.4751 Å20 Å2
3----2.1732 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.387 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17918 0 256 170 18344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918543
X-RAY DIFFRACTIONf_angle_d1.49125148
X-RAY DIFFRACTIONf_chiral_restr0.1142766
X-RAY DIFFRACTIONf_plane_restr0.0053206
X-RAY DIFFRACTIONf_dihedral_angle_d16.4796952
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2250X-RAY DIFFRACTIONPOSITIONAL0.098
12B2250X-RAY DIFFRACTIONPOSITIONAL0.098
13C2208X-RAY DIFFRACTIONPOSITIONAL0.1
14D2217X-RAY DIFFRACTIONPOSITIONAL0.126
15I2250X-RAY DIFFRACTIONPOSITIONAL0.056
16J2250X-RAY DIFFRACTIONPOSITIONAL0.176
17K2214X-RAY DIFFRACTIONPOSITIONAL0.067
18L2217X-RAY DIFFRACTIONPOSITIONAL0.104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6003-2.67060.39471100.31833917402766
2.6706-2.74920.46451240.28834244436871
2.7492-2.83790.36361230.26864667479078
2.8379-2.93930.33271310.25865105523686
2.9393-3.05690.35711440.27165460560491
3.0569-3.1960.36771480.26215606575494
3.196-3.36450.36931510.24255800595196
3.3645-3.57520.27991540.22565807596197
3.5752-3.85110.25371540.20985886604098
3.8511-4.23830.2411590.16635953611298
4.2383-4.85090.20291610.149760426203100
4.8509-6.10890.21981620.174661246286100
6.1089-43.39260.19131680.16816317648599

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