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- PDB-3oh1: Protein structure of USP from L. major bound to URIDINE-5'-DIPHOS... -

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Basic information

Entry
Database: PDB / ID: 3oh1
TitleProtein structure of USP from L. major bound to URIDINE-5'-DIPHOSPHATE-Galacturonic acid
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-UGB / UTP-monosaccharide-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 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)71,3044
Polymers70,5401
Non-polymers7643
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.226, 122.320, 61.221
Angle α, β, γ (deg.)90.000, 105.420, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

21A-691-

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-UGB / (2S,3R,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4,5-trihydroxy-oxane-2-carboxylic acid


Mass: 580.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N2O18P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
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: 14.1 / 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: 2.18→50 Å / Num. all: 39888 / Num. obs: 39879 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 33.68 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.044 / Χ2: 1.009 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.18-2.265.70.30140221.038100
2.26-2.355.80.42139511.02199.3
2.35-2.466.40.18340010.953100
2.46-2.586.50.11939640.996100
2.58-2.756.40.08840060.994100
2.75-2.966.50.05839741.082100
2.96-3.266.50.04440201.008100
3.26-3.736.40.03740041.008100
3.73-4.76.40.02640260.99100
4.7-506.10.02439111.00696.3

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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: 2.18→29.509 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 1840 4.87 %RANDOM
Rwork0.1996 ---
obs0.2017 37777 94.2 %-
all-39879 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.856 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 257.93 Å2 / Biso mean: 60.5152 Å2 / Biso min: 24.11 Å2
Baniso -1Baniso -2Baniso -3
1-8.0927 Å2-0 Å2-0.8422 Å2
2---8.1125 Å20 Å2
3---0.0198 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.33 Å
Luzzati d res low-8 Å
Luzzati sigma a0.35 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.18→29.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4522 0 49 219 4790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134700
X-RAY DIFFRACTIONf_angle_d1.3766397
X-RAY DIFFRACTIONf_chiral_restr0.09736
X-RAY DIFFRACTIONf_plane_restr0.006826
X-RAY DIFFRACTIONf_dihedral_angle_d19.0371769
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 (%)
2.18-2.23750.5912940.57591877197164
2.2375-2.30330.54931420.5172419256183
2.3033-2.37760.36881330.29562505263886
2.3776-2.46260.25731500.20642885303599
2.4626-2.56110.22481450.186129193064100
2.5611-2.67760.25311670.192528963063100
2.6776-2.81870.27951490.191729233072100
2.8187-2.99510.26721520.194129323084100
2.9951-3.22610.19391460.178129213067100
3.2261-3.55030.22381390.17332921306099
3.5503-4.06290.19331480.16442923307199
4.0629-5.11450.17171290.136729773106100
5.1145-29.51130.17061460.15032839298596
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)
13.80710.5472-1.28680.91430.33081.44350.2088-0.13950.28340.5636-0.16050.35990.5597-0.19130.01370.5655-0.26750.15680.5203-0.09750.6457.805229.880148.4837
21.45060.53991.17020.67181.05921.8303-0.3940.14270.9949-0.67610.024-0.3955-1.25380.45050.27110.9982-0.4450.03870.5730.03311.275931.126912.816324.5405
31.2525-0.25230.27252.1650.31972.08980.1767-0.01120.0711-0.0199-0.1593-0.3028-0.0860.0069-0.01010.2657-0.0480.01240.27060.04750.23539.521-6.632724.5975
41.25740.22431.10180.50910.871.9208-0.05450.2722-0.2702-0.31420.11770.0834-0.42360.3569-0.07060.7127-0.2057-0.11410.5179-0.02820.452814.778625.861530.2983
52.64181.4560.99771.10450.52760.7179-0.0250.13630.3607-0.1617-0.41480.82720.1857-0.30820.37510.5253-0.2112-0.05140.4809-0.1420.77865.74825.654538.0471
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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