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- PDB-3oh4: Protein structure of USP from L. major bound to URIDINE-5'-DIPHOS... -

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Basic information

Entry
Database: PDB / ID: 3oh4
TitleProtein structure of USP from L. major bound to URIDINE-5'-DIPHOSPHATE Glucose
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
URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP-monosaccharide-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.21 Å
AuthorsDickmanns, A. / Damerow, S. / Neumann, P. / Schulz, E.-C. / Lamerz, A. / Routier, F.H. / 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

Downloads & links

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Assembly

Deposited unit
A: UDP-sugar pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1983
Polymers70,5401
Non-polymers6582
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)107.814, 121.665, 61.393
Angle α, β, γ (deg.)90.000, 105.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-712-

HOH

21A-728-

HOH

31A-758-

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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / 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: 2.75 Å3/Da / Density % sol: 55.23 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9814 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9814 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 37828 / Num. obs: 37828 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 42.17 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.052 / Χ2: 1.007 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.21-2.340.50237071.02298.4
2.3-2.394.30.43737871.02999.8
2.39-2.54.40.30737691.017100
2.5-2.634.50.22438071.005100
2.63-2.84.50.15437841.002100
2.8-3.014.50.09437790.992100
3.01-3.324.50.05937840.997100
3.32-3.84.50.03937901100
3.8-4.784.50.02838270.996100
4.78-504.40.02537941.01198.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3OGZ

3ogz


Resolution: 2.21→32.891 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.31 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 1839 4.87 %RANDOM
Rwork0.1784 ---
obs0.18 37766 99.14 %-
all-37766 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.673 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 216.23 Å2 / Biso mean: 61.0035 Å2 / Biso min: 24.08 Å2
Baniso -1Baniso -2Baniso -3
1-9.7861 Å2-0 Å2-6.9762 Å2
2---7.585 Å2-0 Å2
3----2.2011 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.31 Å
Luzzati d res low-8 Å
Luzzati sigma a0.33 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.21→32.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 42 219 4808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054751
X-RAY DIFFRACTIONf_angle_d0.8816466
X-RAY DIFFRACTIONf_chiral_restr0.06737
X-RAY DIFFRACTIONf_plane_restr0.003841
X-RAY DIFFRACTIONf_dihedral_angle_d17.3541798
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 (%)
2.21-2.26970.32881450.26542575272093
2.2697-2.33650.28161370.22082735287299
2.3365-2.41190.23911430.20822736287999
2.4119-2.4980.27181430.194927972940100
2.498-2.5980.27011570.202427422899100
2.598-2.71620.23851460.203828002946100
2.7162-2.85930.24371390.197127532892100
2.8593-3.03830.23191290.196428002929100
3.0383-3.27270.24651320.187728032935100
3.2727-3.60170.2021250.178828142939100
3.6017-4.1220.19021520.154427872939100
4.122-5.19010.15131430.133827962939100
5.1901-32.89470.18221480.15952789293798
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)
12.43750.2909-1.03580.64540.19581.45760.03020.00540.23160.29930.07310.10790.7325-0.3819-0.06120.5937-0.29340.02550.6611-0.04030.57127.333129.684748.4325
22.75372.11660.85182.07760.94410.45740.1766-0.1910.492-0.3983-0.2566-0.5612-0.75260.5977-0.0160.8245-0.48640.03070.78630.01610.879530.533413.481124.6998
31.2651-0.15590.47831.74190.19162.85330.1317-0.08330.01550.0714-0.1511-0.1658-0.08050.0840.01890.2882-0.07850.00930.32820.05480.26489.4513-6.74424.8297
40.0824-0.0599-0.07630.2830.30460.32880.08280.08530.147-0.46470.01330.2145-0.1485-0.0332-0.09270.8705-0.1852-0.1060.51160.02510.577614.390125.655830.2406
51.2031-0.10130.45570.1377-0.2420.77170.03430.01410.1959-0.3045-0.16720.25430.3943-0.25240.08850.5808-0.2313-0.13150.5266-0.09860.5575.221425.674938.0894
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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