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- PDB-6n0u: Crystal structure of a glucose-1-phosphate thymidylyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 6n0u
TitleCrystal structure of a glucose-1-phosphate thymidylyltransferase from Burkholderia phymatum bound to 2'-deoxy-thymidine-B-L-rhamnose
ComponentsGlucose-1-phosphate thymidylyltransferase
KeywordsTRANSFERASE / NIAID / structural genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / extracellular polysaccharide biosynthetic process / metal 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'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE / Glucose-1-phosphate thymidylyltransferase
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a glucose-1-phosphate thymidylyltransferase from Burkholderia phymatum bound to 2'-deoxy-thymidine-B-L-rhamnose
Authors: Edwards, T.E. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)138,77210
Polymers136,4554
Non-polymers2,3176
Water8,845491
1
A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules

A: Glucose-1-phosphate thymidylyltransferase
B: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,77210
Polymers136,4554
Non-polymers2,3176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area16760 Å2
ΔGint-62 kcal/mol
Surface area40910 Å2
MethodPISA
2
C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules

C: Glucose-1-phosphate thymidylyltransferase
D: Glucose-1-phosphate thymidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,77210
Polymers136,4554
Non-polymers2,3176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area16490 Å2
ΔGint-54 kcal/mol
Surface area40540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.320, 80.180, 131.040
Angle α, β, γ (deg.)90.000, 123.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-671-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 3 or (resid 4...
21(chain B and (resid 2 through 3 or (resid 4...
31(chain C and (resid 2 through 3 or (resid 4...
41(chain D and (resid 2 through 21 or (resid 22...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARG(chain A and (resid 2 through 3 or (resid 4...AA2 - 310 - 11
12LYSLYSLYSLYS(chain A and (resid 2 through 3 or (resid 4...AA412
13HISHISTRHTRH(chain A and (resid 2 through 3 or (resid 4...AA - E0 - 5008
14HISHISTRHTRH(chain A and (resid 2 through 3 or (resid 4...AA - E0 - 5008
15HISHISTRHTRH(chain A and (resid 2 through 3 or (resid 4...AA - E0 - 5008
16HISHISTRHTRH(chain A and (resid 2 through 3 or (resid 4...AA - E0 - 5008
21ALAALAARGARG(chain B and (resid 2 through 3 or (resid 4...BB2 - 310 - 11
22LYSLYSLYSLYS(chain B and (resid 2 through 3 or (resid 4...BB412
23ALAALATRHTRH(chain B and (resid 2 through 3 or (resid 4...BB - G2 - 50010
31ALAALAARGARG(chain C and (resid 2 through 3 or (resid 4...CC2 - 310 - 11
32LYSLYSLYSLYS(chain C and (resid 2 through 3 or (resid 4...CC412
33METMETEDOEDO(chain C and (resid 2 through 3 or (resid 4...CC - I1 - 5019
34METMETEDOEDO(chain C and (resid 2 through 3 or (resid 4...CC - I1 - 5019
35METMETEDOEDO(chain C and (resid 2 through 3 or (resid 4...CC - I1 - 5019
36METMETEDOEDO(chain C and (resid 2 through 3 or (resid 4...CC - I1 - 5019
41ALAALAHISHIS(chain D and (resid 2 through 21 or (resid 22...DD2 - 2110 - 29
42VALVALVALVAL(chain D and (resid 2 through 21 or (resid 22...DD2230
43ALAALATRHTRH(chain D and (resid 2 through 21 or (resid 22...DD - J2 - 50010
44ALAALATRHTRH(chain D and (resid 2 through 21 or (resid 22...DD - J2 - 50010
45ALAALATRHTRH(chain D and (resid 2 through 21 or (resid 22...DD - J2 - 50010
46ALAALATRHTRH(chain D and (resid 2 through 21 or (resid 22...DD - J2 - 50010

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Components

#1: Protein
Glucose-1-phosphate thymidylyltransferase /


Mass: 34113.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_2318 / Production host: Escherichia coli (E. coli)
References: UniProt: B2JFC5, glucose-1-phosphate thymidylyltransferase
#2: Chemical
ChemComp-TRH / 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE


Mass: 548.330 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H26N2O15P2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 491 / 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: 51.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: BuphA.00118.a.B1.PW38413 at 20.75 mg/mL against Morpheus screen condition D9: 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each alcohol (1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, ...Details: BuphA.00118.a.B1.PW38413 at 20.75 mg/mL against Morpheus screen condition D9: 10% PEG 20,000, 20% PEG 550 MME, 0.02 M each alcohol (1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol), 0.1 M bicine/Trizma pH 8.5, crystal tracking ID 299441d9, unique puck ID bcs8-10

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→42.327 Å / Num. obs: 76630 / % possible obs: 99.2 % / Redundancy: 4.914 % / Biso Wilson estimate: 43.493 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.063 / Χ2: 1.028 / Net I/σ(I): 16.15 / Num. measured all: 376578 / Scaling rejects: 1097
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.155.0350.5172.9128566569456730.9360.57899.6
2.15-2.214.9920.5632.6727213550554510.940.6399
2.21-2.284.3740.4124.4222382538651170.9650.47295
2.28-2.354.8590.3554.2125155521051770.9710.39999.4
2.35-2.425.0860.2535.6526021512951160.9810.28399.7
2.42-2.515.1260.1937.2524926487248630.9870.21599.8
2.51-2.65.1030.1479.2324189475447400.9940.16499.7
2.6-2.715.0990.12710.7323221456445540.9940.14299.8
2.71-2.835.0780.10513.2822161437243640.9950.11799.8
2.83-2.975.060.0816.6621350423342190.9970.0999.7
2.97-3.135.0170.06719.8719702393339270.9970.07599.8
3.13-3.324.9210.05423.9818698381338000.9980.06199.7
3.32-3.554.8560.04527.8417167354135350.9980.0599.8
3.55-3.834.5430.04130.0414784329632540.9980.04798.7
3.83-4.24.7220.0343614368305130430.9990.03899.7
4.2-4.74.7590.03139.0913183277727700.9990.03599.7
4.7-5.424.7510.02940.4211645246424510.9990.03299.5
5.42-6.644.8140.02840.679936207720640.9990.03299.4
6.64-9.394.8180.02443.837824162916240.9990.02799.7
9.39-42.3274.6020.02344.440879328880.9990.02695.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX(1.14_3260)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFY

5ify


Resolution: 2.1→42.327 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.53
RfactorNum. reflection% reflection
Rfree0.2331 4265 6.07 %
Rwork0.182 --
obs0.1851 70291 91.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.02 Å2 / Biso mean: 52.814 Å2 / Biso min: 12.2 Å2
Refinement stepCycle: final / Resolution: 2.1→42.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8902 0 148 496 9546
Biso mean--43.64 45.89 -
Num. residues----1171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099292
X-RAY DIFFRACTIONf_angle_d1.2412707
X-RAY DIFFRACTIONf_dihedral_angle_d13.2815537
X-RAY DIFFRACTIONf_chiral_restr0.0641438
X-RAY DIFFRACTIONf_plane_restr0.0081675
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4939X-RAY DIFFRACTION8.324TORSIONAL
12B4939X-RAY DIFFRACTION8.324TORSIONAL
13C4939X-RAY DIFFRACTION8.324TORSIONAL
14D4939X-RAY DIFFRACTION8.324TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0999-2.12380.36121330.29451997213083
2.1238-2.14880.32231210.27442017213884
2.1488-2.1750.30591270.27982003213084
2.175-2.20250.28611220.30311866198878
2.2025-2.23150.4476840.35511280136453
2.2315-2.26210.51091480.45012009215784
2.2621-2.29440.3822930.3631384147758
2.2944-2.32860.29851470.24672080222787
2.3286-2.3650.31141290.24942116224589
2.365-2.40380.29231340.22932200233491
2.4038-2.44520.28151450.21672205235092
2.4452-2.48970.25721370.19462257239494
2.4897-2.53760.27061360.19022296243294
2.5376-2.58940.24151620.19442252241494
2.5894-2.64570.26111460.1922263240995
2.6457-2.70720.24671450.20212324246996
2.7072-2.77490.26331540.19512370252497
2.7749-2.84990.24221430.192347249097
2.8499-2.93370.25041570.19292303246097
2.9337-3.02840.23731560.18792370252699
3.0284-3.13660.24341690.19232357252698
3.1366-3.26210.24131270.19772408253599
3.2621-3.41050.23981370.18732415255299
3.4105-3.59030.25741690.18312379254899
3.5903-3.81510.20591630.16072320248397
3.8151-4.10940.16561420.13212424256699
4.1094-4.52250.17741300.123424642594100
4.5225-5.1760.17261730.122623942567100
5.176-6.51730.21111750.154224462621100
6.5173-42.33520.16831610.14512480264199
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)
12.80880.66953.28741.38650.70384.06320.43690.4937-0.9514-0.04820.169-0.09670.22490.346-0.39650.29970.02490.03290.2112-0.11260.388130.9284-40.478541.5393
21.84820.34910.81081.5580.40452.41960.31150.067-0.9295-0.03970.0153-0.14770.479-0.0159-0.2130.28550.0006-0.04740.1607-0.04150.487328.2189-43.04145.5918
32.34160.65820.68523.00570.73522.4882-0.1893-0.1066-0.0261-0.10810.07490.27310.0782-0.2566-0.00570.2032-0.02130.00420.1846-0.01880.198919.2832-28.486442.0782
42.09630.20080.73021.4631-0.05161.90870.00270.5786-0.2838-0.38130.0624-0.00890.09170.1385-0.02410.2316-0.00440.0180.3277-0.09320.223927.8104-29.463632.3462
53.08661.49210.40843.0783-0.07062.68560.2476-0.4508-0.32650.43840.0730.36250.5154-0.6634-0.10850.2915-0.05810.05780.34350.06040.389916.7072-36.071559.5231
62.609-2.35071.00142.7674-2.42666.75490.0839-1.73350.84380.74780.88640.0277-0.9028-0.4263-0.75450.5555-0.0150.14330.6656-0.11030.547519.2501-30.10565.1196
77.1192-0.23823.86520.3719-0.22732.6871-0.6622-0.49471.01720.1710.08390.0423-0.2488-0.27080.61840.36940.0769-0.0070.2376-0.10660.488329.72392.839458.6489
82.78230.00680.36721.7438-0.35081.184-0.15780.08160.9928-0.0099-0.1070.0973-0.4141-0.13730.10880.31780.0365-0.07260.1781-0.04110.547224.38123.839549.8403
93.8415-0.31460.1542.5015-0.02713.1039-0.0879-0.33220.2004-0.0537-0.02170.44370.0516-0.31270.11180.22630.02850.01460.2602-0.09490.369711.7476-10.961755.5669
103.19050.0560.19351.56920.00211.6186-0.1445-0.15690.52790.0208-0.00550.1984-0.2263-0.21130.08550.19650.0421-0.01610.1774-0.09940.315719.4163-5.378852.6624
116.6854.25483.35526.55592.60816.5314-0.53452.01040.2526-0.82320.9036-0.0315-0.0399-0.0169-0.35380.4797-0.09150.06640.68280.05190.348634.8521-7.359731.519
122.39321.34450.00967.9804-2.13820.66110.2776-0.74440.09720.6493-0.08880.2493-0.3516-0.2006-0.17830.55260.01190.08440.7703-0.0290.2273-16.6256-17.185715.6882
131.8155-0.39560.91762.1184-0.85632.00170.0365-0.199-0.00720.15030.15270.2777-0.0237-0.526-0.19660.41230.01920.03080.73390.05030.2377-19.8313-23.991811.2894
143.69841.9203-0.28273.0523-0.05983.88870.16870.0165-0.5457-0.2138-0.0561-0.00720.2912-0.1906-0.10890.4339-0.0114-0.09140.67350.03780.3098-7.1569-36.909210.9197
156.9081-4.0823-0.63814.48261.79144.36850.2694-0.1949-0.0948-0.72130.2203-0.0506-0.47320.1288-0.45130.4206-0.1288-0.01570.6492-0.02270.20684.6601-29.151719.7603
161.71-0.29050.16320.5614-0.3031.99540.1835-0.2666-0.13380.1028-0.02930.0524-0.111-0.0712-0.14490.4161-0.0180.00660.57640.02170.2355-9.6278-27.231711.4244
176.6067-4.2075-2.23396.66123.86452.24320.0305-0.4397-0.37450.08150.13520.26740.05770.1754-0.14230.44990.0862-0.06150.72350.02170.2439-17.35-23.2028-12.0987
182.6865-0.59230.41524.51420.05211.65390.2015-0.12970.8661-0.0916-0.31850.2162-0.7602-0.63850.1430.6460.1450.0920.6131-0.06850.4893-17.97841.62344.9743
192.033-0.28730.6242.3541-1.27932.3990.0056-0.66840.5590.8477-0.05680.5521-0.7636-0.91160.02581.06570.19140.3090.8878-0.30611.0041-25.45066.796810.902
201.7207-0.446-0.1462.64790.15672.61070.1078-0.26580.95860.1471-0.19290.3619-0.9285-0.33950.02860.99440.1967-0.04090.5048-0.09551.1898-18.174216.77140.5528
215.419-0.88680.83896.61492.15394.1162-0.0440.46450.4916-0.1553-0.22220.7403-0.822-0.42870.25350.93730.2423-0.0660.56470.0890.867-20.468513.7369-12.1603
221.94970.28521.41692.2391-0.15613.087-0.09050.32630.913-0.1663-0.24970.3329-0.5465-0.05370.34950.65350.06750.01680.49220.07630.6142-10.50299.1875-3.6771
235.746-0.8144-2.25434.5727-3.66718.1741-0.4256-1.42710.91711.27670.4511-0.4141-0.8544-0.2407-0.11371.10250.0205-0.03080.8049-0.2060.5972-7.34298.345921.332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )A0 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 108 )A19 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 127 )A109 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 246 )A128 - 246
5X-RAY DIFFRACTION5chain 'A' and (resid 247 through 275 )A247 - 275
6X-RAY DIFFRACTION6chain 'A' and (resid 276 through 294 )A276 - 294
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 24 )B2 - 24
8X-RAY DIFFRACTION8chain 'B' and (resid 25 through 117 )B25 - 117
9X-RAY DIFFRACTION9chain 'B' and (resid 118 through 155 )B118 - 155
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 275 )B156 - 275
11X-RAY DIFFRACTION11chain 'B' and (resid 276 through 294 )B276 - 294
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 24 )C1 - 24
13X-RAY DIFFRACTION13chain 'C' and (resid 25 through 117 )C25 - 117
14X-RAY DIFFRACTION14chain 'C' and (resid 118 through 138 )C118 - 138
15X-RAY DIFFRACTION15chain 'C' and (resid 139 through 155 )C139 - 155
16X-RAY DIFFRACTION16chain 'C' and (resid 156 through 275 )C156 - 275
17X-RAY DIFFRACTION17chain 'C' and (resid 276 through 295 )C276 - 295
18X-RAY DIFFRACTION18chain 'D' and (resid 2 through 45 )D2 - 45
19X-RAY DIFFRACTION19chain 'D' and (resid 46 through 87 )D46 - 87
20X-RAY DIFFRACTION20chain 'D' and (resid 88 through 138 )D88 - 138
21X-RAY DIFFRACTION21chain 'D' and (resid 139 through 198 )D139 - 198
22X-RAY DIFFRACTION22chain 'D' and (resid 199 through 246 )D199 - 246
23X-RAY DIFFRACTION23chain 'D' and (resid 247 through 289 )D247 - 289

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