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- PDB-3dmp: 2.6 A crystal structure of uracil phosphoribosyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 3dmp
Title2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / BURKHOLDERIA / PSEUDOMALLEI / URACIL / PHOSPHORIBOSYLTRANSFERASE / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / Glycosyltransferase / Magnesium
Function / homology
Function and homology information


uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / nucleoside metabolic process / GTP binding / magnesium ion binding
Similarity search - Function
Uracil phosphoribosyltransferase, bacterial-type / Uracil phosphoribosyl transferase / Uracil phosphoribosyltransferase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)96,7884
Polymers96,7884
Non-polymers00
Water1,49583
1
A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase

A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)96,7884
Polymers96,7884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12390 Å2
ΔGint-59 kcal/mol
Surface area31930 Å2
MethodPISA
2
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase

C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)96,7884
Polymers96,7884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12520 Å2
ΔGint-65 kcal/mol
Surface area32250 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.222, 80.637, 141.833
Angle α, β, γ (deg.)90.00, 99.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uracil phosphoribosyltransferase / UMP pyrophosphorylase / UPRTase


Mass: 24197.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710B / Gene: upp, BPSL1166 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q63VS8, uracil phosphoribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 2M NaCl, 5% PEG 4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 39360 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 4.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.5-2.593.70.764100
2.59-2.693.80.663100
2.69-2.823.80.524100
2.82-2.963.80.402100
2.96-3.153.80.30899.9
3.15-3.393.80.21699.7
3.39-3.733.70.15899.5
3.73-4.273.70.12899.3
4.27-5.383.60.10299.1
5.38-503.70.08199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 60.03 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.32 Å
Translation3 Å49.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.445 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27053 1758 5 %RANDOM
Rwork0.21882 ---
obs0.22145 33305 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.02 Å2
2--0 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6694 0 0 83 6777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.999274
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85322.441295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.261151175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7641568
X-RAY DIFFRACTIONr_chiral_restr0.0950.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025122
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.22971
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24534
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.2201
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5811.54359
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02726917
X-RAY DIFFRACTIONr_scbond_it1.36332679
X-RAY DIFFRACTIONr_scangle_it2.34.52357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 126 -
Rwork0.311 2412 -
obs--99.88 %

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