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- PDB-1v9s: Crystal structure of TT0130 protein from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1v9s
TitleCrystal structure of TT0130 protein from Thermus thermophilus HB8
Componentsuracil phosphoribosyltransferase
KeywordsTRANSFERASE / pyrimidine salvage / oligomerization / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsLokanath, N.K. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of uracil phosphoribosyltransferase from Thermus thermophilus HB8
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionJan 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: uracil phosphoribosyltransferase
B: uracil phosphoribosyltransferase
C: uracil phosphoribosyltransferase
D: uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,70527
Polymers92,4964
Non-polymers2,20923
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18500 Å2
ΔGint-456 kcal/mol
Surface area29410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.151, 116.151, 157.643
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is homotetramer composed of four protomers in the asymmetric unit.

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Components

#1: Protein
uracil phosphoribosyltransferase


Mass: 23123.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q72J35, uracil phosphoribosyltransferase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 3.2 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.5
Details: ammonium sulphate, sodium citrate, dioxane, pH 5.5, microbatch, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97874, 0.97914, 0.98400, 1.00
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 8, 2003 / Details: RH COATED BENT-CYRINDRICAL MIRROR
RadiationMonochromator: SI111 DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978741
20.979141
30.9841
411
ReflectionResolution: 2.1→30 Å / Num. all: 71936 / Num. obs: 71836 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.294 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 3646 -random
Rwork0.238 ---
all0.24 71936 --
obs0.24 71836 99.9 %-
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å2-1.69 Å20 Å2
2---2.81 Å20 Å2
3---5.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6233 0 115 369 6717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.35 431 -
Rwork0.312 --
obs-8818 98.9 %

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