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- PDB-3oh3: Protein structure of USP from L. major bound to URIDINE-5'-DIPHOS... -

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Basic information

Entry
Database: PDB / ID: 3oh3
TitleProtein structure of USP from L. major bound to URIDINE-5'-DIPHOSPHATE -Arabinose
ComponentsUDP-sugar pyrophosphorylase
KeywordsTRANSFERASE / left handed beta helix / Rossmann Fold / UDP sugar pyrophosphorylase
Function / homology
Function and homology information


UTP-monosaccharide-1-phosphate uridylyltransferase / uridylyltransferase activity
Similarity search - Function
UDP N-Acetylglucosamine Acyltransferase; domain 1 - #30 / UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex ...UDP N-Acetylglucosamine Acyltransferase; domain 1 - #30 / UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-UAD / UTP-monosaccharide-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 Å
AuthorsDickmanns, A. / Damerow, S. / Neumann, P. / Schulz, E.-C. / Lamerz, A. / Routier, F. / Ficner, R.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural basis for the broad substrate range of the UDP-sugar pyrophosphorylase from Leishmania major.
Authors: Dickmanns, A. / Damerow, S. / Neumann, P. / Schulz, E.C. / Lamerz, A.C. / Routier, F.H. / Ficner, R.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / 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

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Assembly

Deposited unit
A: UDP-sugar pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2604
Polymers70,5401
Non-polymers7203
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.161, 122.508, 61.061
Angle α, β, γ (deg.)90.000, 105.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-659-

HOH

21A-719-

HOH

31A-726-

HOH

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Components

#1: Protein UDP-sugar pyrophosphorylase


Mass: 70539.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: 5ASKH / Gene: USP / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D3G6S4, UTP-monosaccharide-1-phosphate uridylyltransferase
#2: Chemical ChemComp-UAD / [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2S,3R,4S,5S)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate


Mass: 536.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O16P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1-0.2 M sodium tartrate, 16-20% PEG5000, 10 mM DTT, pH 7-8, vapor diffusion, sitting drop, temperature 292K
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 48590 / Num. obs: 48590 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 36.98 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.039 / Χ2: 0.996 / Net I/σ(I): 17.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.03-2.094.40.49648420.99799.8
2.09-2.184.50.34448440.999100
2.18-2.274.50.24248510.99999.9
2.27-2.394.50.15848280.996100
2.39-2.544.50.10648730.997100
2.54-2.744.50.07548600.99100
2.74-3.024.50.04648860.997100
3.02-3.454.50.0348620.999100
3.45-4.354.50.02249020.986100
4.35-504.40.01948421.00298.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3OGZ

3ogz


Resolution: 2.03→27.173 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.24 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 2374 4.89 %RANDOM
Rwork0.1756 ---
obs0.177 48579 99.14 %-
all-48590 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.32 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 213.29 Å2 / Biso mean: 52.5145 Å2 / Biso min: 20.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.7527 Å2-0 Å2-2.9723 Å2
2---5.1655 Å20 Å2
3---4.4128 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-8 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.03→27.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 46 338 4931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044748
X-RAY DIFFRACTIONf_angle_d0.8936461
X-RAY DIFFRACTIONf_chiral_restr0.063736
X-RAY DIFFRACTIONf_plane_restr0.003840
X-RAY DIFFRACTIONf_dihedral_angle_d16.8611790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.07120.32411140.26182438255289
2.0712-2.11620.28181320.23727122844100
2.1162-2.16550.26331480.220827382886100
2.1655-2.21960.26941270.215327162843100
2.2196-2.27960.22341420.204527522894100
2.2796-2.34660.23891350.194327382873100
2.3466-2.42230.22941450.187927252870100
2.4223-2.50880.21871510.175127302881100
2.5088-2.60920.22371390.184327142853100
2.6092-2.72780.22821510.188927622913100
2.7278-2.87150.21461490.187726962845100
2.8715-3.05120.22041540.183427642918100
3.0512-3.28640.19881430.175427142857100
3.2864-3.61650.20481340.163727632897100
3.6165-4.13820.19431420.149427372879100
4.1382-5.20770.13591260.138527882914100
5.2077-27.17510.17641420.16952718286097
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)
11.51090.4004-0.4760.7527-0.07691.38080.10410.0030.54090.12820.03370.41310.3428-0.1526-0.11670.3725-0.1890.10610.3782-0.06950.58927.344830.392748.1304
21.44251.38630.34781.48350.48950.2409-0.19370.04650.9529-0.79670.0793-0.3569-0.84520.30680.00460.6633-0.25430.04490.4750.05291.281731.118513.494224.457
31.1056-0.39880.1851.99310.4581.41770.17690.00880.0679-0.0459-0.1555-0.3303-0.0338-0.0396-0.0180.2144-0.01720.02260.22920.04520.2149.4792-6.21824.5543
40.4554-0.41610.49431.0311-0.11420.96220.11790.28870.0291-0.3790.00720.2458-0.41270.1961-0.01840.6023-0.1103-0.1040.39140.0050.421814.75426.166530.0623
50.69280.52620.12620.70380.31790.30220.05610.1750.1751-0.2667-0.27790.82990.0543-0.2670.20810.3601-0.1004-0.08670.4031-0.08960.65555.609326.149337.7739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 1:76)A1 - 76
2X-RAY DIFFRACTION2chain A and (resid 77:85 or resid 300:356)A77 - 85
3X-RAY DIFFRACTION2chain A and (resid 77:85 or resid 300:356)A300 - 356
4X-RAY DIFFRACTION3chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A86 - 195
5X-RAY DIFFRACTION3chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A224 - 299
6X-RAY DIFFRACTION3chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A357 - 378
7X-RAY DIFFRACTION3chain A and (resid 86:195 or resid 224:299 or resid 357:378 or resid 406:615)A406 - 615
8X-RAY DIFFRACTION4chain A and (resid 379:405)A379 - 405
9X-RAY DIFFRACTION5chain A and (resid 196:223)A196 - 223

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