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- PDB-3oh2: Protein structure of USP from L. major bound to URIDINE-5'-DIPHOS... -

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Basic information

Entry
Database: PDB / ID: 3oh2
TitleProtein structure of USP from L. major bound to URIDINE-5'-DIPHOSPHATE-GALACTOSE
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
GALACTOSE-URIDINE-5'-DIPHOSPHATE / UTP-monosaccharide-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.14 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

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
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.433, 121.910, 61.407
Angle α, β, γ (deg.)90.000, 105.980, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-680-

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-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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.: 253 / 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: 14.1 / 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: 2.14→30 Å / Num. all: 41738 / Num. obs: 41738 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 41.14 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.053 / Χ2: 1.001 / Net I/σ(I): 22
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.14-2.224.30.35942130.994100
2.22-2.314.30.23542040.993100
2.31-2.414.30.16841680.992100
2.41-2.544.30.11342010.992100
2.54-2.74.30.08142141.005100
2.7-2.94.30.05442181.005100
2.9-3.24.30.0441931.01899.9
3.2-3.664.20.04741771.00799.6
3.66-4.613.80.04741651.00698.1
4.61-3040.03839850.99493.3

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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: 2.14→29.517 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8497 / SU ML: 0.24 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.33 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 2113 5.06 %RANDOM
Rwork0.1679 ---
obs0.1697 41728 98.72 %-
all-41728 --
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.751 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 188.3 Å2 / Biso mean: 60.9787 Å2 / Biso min: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-12.5713 Å2-0 Å2-9.0136 Å2
2---10.9628 Å2-0 Å2
3----1.6085 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: 2.14→29.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 0 42 253 4799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014676
X-RAY DIFFRACTIONf_angle_d1.2716361
X-RAY DIFFRACTIONf_chiral_restr0.083730
X-RAY DIFFRACTIONf_plane_restr0.005822
X-RAY DIFFRACTIONf_dihedral_angle_d17.7151763
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.14-2.18240.24291240.19742538266295
2.1824-2.23690.22681330.186726572790100
2.2369-2.29740.22531490.183526832832100
2.2974-2.3650.25541350.1826442779100
2.365-2.44130.22581390.17827072846100
2.4413-2.52850.20711360.173326392775100
2.5285-2.62960.26261590.191226752834100
2.6296-2.74920.25821550.198426332788100
2.7492-2.89410.25011490.200326942843100
2.8941-3.07520.23321490.189826552804100
3.0752-3.31240.21211260.184926682794100
3.3124-3.64510.21371560.16322653280999
3.6451-4.17130.17251530.14592639279299
4.1713-5.25060.14181360.12642622275897
5.2506-29.51990.17841140.15932508262291
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)
12.50350.3637-1.02170.69360.1711.18170.079-0.08650.24750.2446-0.01270.15390.5279-0.3414-0.0620.5489-0.28430.0660.6752-0.11380.62067.073629.982147.9936
21.96491.5483-0.23493.1550.09530.06150.2879-0.02430.5887-0.41630.0071-1.0891-0.80090.7895-0.25210.6737-0.37160.06740.7539-0.0090.926629.738313.063724.8191
31.4131-0.07210.39571.88410.37822.41120.1589-0.07810.0020.0491-0.1504-0.2278-0.07150.0726-0.00680.1715-0.07060.02570.27490.05760.19759.4399-6.659224.96
40.5526-0.16150.43290.18340.08330.658-0.0530.2392-0.1085-0.2119-0.04020.2811-0.23490.11840.06750.7052-0.1705-0.13730.5013-0.01740.571714.343625.810330.1066
52.03731.62720.13041.58730.56380.7090.09110.14950.5944-0.192-0.2730.55240.1142-0.41960.2090.5182-0.1713-0.08580.5836-0.09640.71985.17525.716937.7943
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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