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- PDB-2ehj: Structure of Uracil phosphoribosyl transferase -

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Basic information

Entry
Database: PDB / ID: 2ehj
TitleStructure of Uracil phosphoribosyl transferase
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / uracil phosphoribosyl transferase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / pyrimidine nucleobase metabolic process / UMP salvage / guanosine tetraphosphate binding / GTP binding / magnesium ion binding / identical protein binding / membrane ...uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / pyrimidine nucleobase metabolic process / UMP salvage / guanosine tetraphosphate binding / GTP binding / magnesium ion binding / identical protein binding / membrane / cytosol / cytoplasm
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLokanath, N.K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of Uracil phosphoribosyl transferase
Authors: Lokanath, N.K. / Pampa, K.J. / Kamiya, T. / Kunishima, N.
History
DepositionMar 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 25, 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: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,05823
Polymers90,2334
Non-polymers1,82519
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,07712
Polymers45,1162
Non-polymers96110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-179 kcal/mol
Surface area17960 Å2
MethodPISA
3
B: Uracil phosphoribosyltransferase
C: Uracil phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,98111
Polymers45,1162
Non-polymers8659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-160 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.312, 91.312, 266.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Uracil phosphoribosyltransferase / UMP pyrophosphorylase / UPRTase


Mass: 22558.236 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: cell-free synthesis / Production host: Escherichia coli (E. coli)
References: UniProt: P0A8F0, uracil phosphoribosyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.05M MES, 1.5M NH2SO4, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 4, 2006 / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. all: 28689 / Num. obs: 28400 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 58 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.3
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V9S

1v9s


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.921 / SU B: 22.953 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.442 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1447 5.1 %RANDOM
Rwork0.21 ---
obs0.21 26956 99.01 %-
all-28689 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.382 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20 Å2
2--1.65 Å20 Å2
3----3.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6324 0 95 85 6504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226492
X-RAY DIFFRACTIONr_angle_refined_deg1.3882.0168794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.2325828
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.27325.345232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.679151208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6311528
X-RAY DIFFRACTIONr_chiral_restr0.0950.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024616
X-RAY DIFFRACTIONr_nbd_refined0.270.23152
X-RAY DIFFRACTIONr_nbtor_refined0.3330.24508
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2199
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.21
X-RAY DIFFRACTIONr_mcbond_it1.2671.54189
X-RAY DIFFRACTIONr_mcangle_it2.19526676
X-RAY DIFFRACTIONr_scbond_it3.57132469
X-RAY DIFFRACTIONr_scangle_it6.0714.52118
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 89 -
Rwork0.307 1737 -
obs--96.38 %
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)
10.52520.1608-0.07040.837-0.27340.8371-0.0308-0.0110.0480.02390.0094-0.0107-0.07550.0110.0213-0.05560.0097-0.0185-0.0594-0.0313-0.012312.336372.5902242.2561
20.6141-0.00740.19310.1645-0.14090.8239-0.00080.04310.0092-0.0204-0.0260.00350.03180.00380.0268-0.03-0.02140.0126-0.0635-0.0268-0.025117.916552.7109224.6627
30.87660.14150.10860.3729-0.06240.5438-0.03670.0205-0.034-0.01750.00880.03230.07820.04350.0278-0.03780.01750.0116-0.0494-0.0103-0.038326.243936.0445246.67
40.60310.0563-0.19710.1915-0.16860.96840.0202-0.06310.01760.0002-0.040.006-0.0321-0.02860.0198-0.05410.02950.0092-0.0356-0.0265-0.036515.971154.167263.8977
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2081 - 208
2X-RAY DIFFRACTION2BB1 - 2081 - 208
3X-RAY DIFFRACTION3CC1 - 2081 - 208
4X-RAY DIFFRACTION4DD1 - 2081 - 208

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