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- PDB-1i5e: CRYSTAL STRUCTURE OF BACILLUS CALDOLYTICUS URACIL PHOSPHORIBOSYLT... -

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Basic information

Entry
Database: PDB / ID: 1i5e
TitleCRYSTAL STRUCTURE OF BACILLUS CALDOLYTICUS URACIL PHOSPHORIBOSYLTRANSFERASE WITH BOUND UMP
ComponentsURACIL PHOSPHORIBOSYLTRANSFERASE
KeywordsTRANSFERASE / uracil phosphoribosyltransferase / salvage pathway / bacillus caldolyticus
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
URIDINE-5'-MONOPHOSPHATE / Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesBacillus caldolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsKadziola, A. / Neuhard, J. / Larsen, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of product-bound Bacillus caldolyticus uracil phosphoribosyltransferase confirms ordered sequential substrate binding.
Authors: Kadziola, A. / Neuhard, J. / Larsen, S.
History
DepositionFeb 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: URACIL PHOSPHORIBOSYLTRANSFERASE
B: URACIL PHOSPHORIBOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3784
Polymers45,7292
Non-polymers6482
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-40 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.4, 89.4, 163.7
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein URACIL PHOSPHORIBOSYLTRANSFERASE / UMP PYROPHOSPHORYLASE


Mass: 22864.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldolyticus (bacteria) / Gene: UPP / Production host: Escherichia coli (E. coli)
References: UniProt: P70881, uracil phosphoribosyltransferase
#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.13 Å3/Da / Density % sol: 70.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, potassium phosphate, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
25 mMinorganic phosphate1drop
36-10 %PEG40001reservoir
40.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.888 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.888 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 13156 / Num. obs: 13156 / % possible obs: 85.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 21.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.31 / % possible all: 90.3
Reflection
*PLUS
Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Highest resolution: 3 Å / % possible obs: 90.3 % / Num. unique obs: 680 / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6.6

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Processing

Software
NameClassification
CCP4model building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 3→40 Å / Cross valid method: R-free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 685 5 %random
Rwork0.223 ---
all-13156 --
obs-13156 85.5 %-
Solvent computationSolvent model: CNS
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.119 Å2-8.932 Å20 Å2
2---10.119 Å20 Å2
3---20.239 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3198 0 42 2 3242
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0075
X-RAY DIFFRACTIONc_angle_deg1.4254
X-RAY DIFFRACTIONc_mcbond_it1.1370.75
X-RAY DIFFRACTIONc_mcangle_it1.4451
X-RAY DIFFRACTIONc_scbond_it1.991
X-RAY DIFFRACTIONc_scangle_it2.3541.25
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 13
RfactorNum. reflection
Rfree0.331 48
Rwork0.3199 1028
obs-1224
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.223 / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.223
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.331 / Rfactor Rwork: 0.3199 / Rfactor obs: 0.3199

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