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- PDB-1u1c: Structure of E. coli uridine phosphorylase complexed to 5-benzyla... -

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Basic information

Entry
Database: PDB / ID: 1u1c
TitleStructure of E. coli uridine phosphorylase complexed to 5-benzylacyclouridine (BAU)
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE / URIDINE SALVAGE / benzylacyclouridine / BAU
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase / nucleotide catabolic process / uridine phosphorylase activity / UMP salvage / potassium ion binding / DNA damage response / protein-containing complex / ATP binding / identical protein binding / cytosol
Similarity search - Function
Uridine phosphorylase / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BAU / : / PHOSPHATE ION / Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBu, W. / Settembre, E.C. / Ealick, S.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines.
Authors: Bu, W. / Settembre, E.C. / el Kouni, M.H. / Ealick, S.E.
History
DepositionJul 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 14, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Uridine phosphorylase
B: Uridine phosphorylase
C: Uridine phosphorylase
D: Uridine phosphorylase
E: Uridine phosphorylase
F: Uridine phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,17321
Polymers164,8286
Non-polymers2,34515
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26390 Å2
ΔGint-188 kcal/mol
Surface area44840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.369, 125.965, 141.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 90 - 220 / Label seq-ID: 93 - 223

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Uridine phosphorylase / / E.C.2.4.2.3 / UrdPase / UPase


Mass: 27471.334 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UDP, B3831 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / References: UniProt: P12758, uridine phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-BAU / 1-((2-HYDROXYETHOXY)METHYL)-5-BENZYLPYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 276.288 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H16N2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.44 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, MES, GLYCEROL, PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→38.07 Å / Num. all: 83127 / Num. obs: 83127 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6 % / Rmerge(I) obs: 0.331 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CNSrefinement
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.07 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.682 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24858 8066 10.1 %RANDOM
Rwork0.2155 ---
all0.21878 72188 --
obs0.21878 72188 96.39 %-
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: 22.732 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2--0.26 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11211 0 153 561 11925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02111551
X-RAY DIFFRACTIONr_angle_refined_deg0.8831.96315687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68151490
X-RAY DIFFRACTIONr_chiral_restr0.060.21873
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028580
X-RAY DIFFRACTIONr_nbd_refined0.1640.25799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2867
X-RAY DIFFRACTIONr_metal_ion_refined0.0010.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.220
X-RAY DIFFRACTIONr_mcbond_it0.1381.57417
X-RAY DIFFRACTIONr_mcangle_it0.259211939
X-RAY DIFFRACTIONr_scbond_it0.35434134
X-RAY DIFFRACTIONr_scangle_it0.6034.53748
Refine LS restraints NCS

Ens-ID: 1 / Number: 964 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.295
2Bloose positional0.185
3Cloose positional0.165
4Dloose positional0.145
5Eloose positional0.145
6Floose positional0.195
1Aloose thermal7.6510
2Bloose thermal1.9210
3Cloose thermal1.3310
4Dloose thermal1.3210
5Eloose thermal1.4310
6Floose thermal1.9510
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 563
Rwork0.254 4923
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)
12.5143-0.2952-0.00131.7395-0.27891.2892-0.06480.2583-0.6767-0.29340.08740.11770.2089-0.155-0.02260.0788-0.04-0.0120.0369-0.01040.22020.682101.974553.0874
22.24520.52030.55872.33140.17821.43880.0942-0.9685-0.04540.7088-0.13920.2451-0.0953-0.41730.04510.299-0.01170.07160.56060.04830.0798-3.8564122.226696.8061
32.21520.48480.10871.7829-0.43671.6766-0.0192-0.6490.56210.5144-0.06090.227-0.4377-0.15680.08010.32960.0878-0.01110.3447-0.21310.2023-1.3728145.848787.6934
41.70310.2083-0.22621.998-0.43632.0972-0.15260.02280.5298-0.05280.09710.3356-0.4546-0.17920.05550.20620.0338-0.14150.03820.0080.2391-3.3561150.310257.1961
51.9771-0.19850.65912.3156-0.35691.4181-0.16130.38390.153-0.51740.08090.007-0.1260.23020.08040.1844-0.077-0.0770.0840.06110.04933.4939131.044541.9667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B3 - 253
2X-RAY DIFFRACTION2C4 - 253
3X-RAY DIFFRACTION3D4 - 253
4X-RAY DIFFRACTION4E3 - 253
5X-RAY DIFFRACTION5F4 - 253

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