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- PDB-1u1d: Structure of e. coli uridine phosphorylase complexed to 5-(phenyl... -

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Basic information

Entry
Database: PDB / ID: 1u1d
TitleStructure of e. coli uridine phosphorylase complexed to 5-(phenylthio)acyclouridine (ptau)
ComponentsUridine phosphorylase
KeywordsTRANSFERASE / PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE / URIDINE SALVAGE / PTAU / 5-(PHENYLTHIO)ACYCLOURIDINE
Function / homology
Function and homology information


UMP catabolic process / uridine catabolic process / uridine phosphorylase / 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-181 / : / PHOSPHATE ION / Uridine phosphorylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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 / 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)167,28121
Polymers164,8286
Non-polymers2,45315
Water9,116506
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26460 Å2
ΔGint-196 kcal/mol
Surface area44870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.150, 125.746, 140.880
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: 2 / 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


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-181 / 1-((2-HYDROXYETHOXY)METHYL)-5-(PHENYLTHIO)PYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 294.326 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C13H14N2O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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→47.14 Å / Num. all: 109591 / Num. obs: 109591 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 %
Reflection shellResolution: 2→2.07 Å / % 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: 2.001→47.14 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.126 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22635 10646 10 %RANDOM
Rwork0.20925 ---
all0.21098 95324 --
obs0.21098 95324 96.73 %-
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: 18.028 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2--0.23 Å20 Å2
3---1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.001→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11273 0 153 506 11932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02111615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8911.96215777
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.81851499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21883
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028636
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1610.25912
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.2840
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.1041.57459
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.204212010
X-RAY DIFFRACTIONr_scbond_it0.36634156
X-RAY DIFFRACTIONr_scangle_it0.6144.53767
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A520tight positional0.010.05
2B520tight positional0.010.05
3C520tight positional0.010.05
4D520tight positional0.010.05
5E520tight positional0.010.05
6F520tight positional0.010.05
1A444medium positional0.080.5
2B444medium positional0.080.5
3C444medium positional0.080.5
4D444medium positional0.070.5
5E444medium positional0.080.5
6F444medium positional0.080.5
1A520tight thermal0.020.5
2B520tight thermal0.010.5
3C520tight thermal0.020.5
4D520tight thermal0.010.5
5E520tight thermal0.010.5
6F520tight thermal0.010.5
1A444medium thermal0.132
2B444medium thermal0.132
3C444medium thermal0.122
4D444medium thermal0.122
5E444medium thermal0.122
6F444medium thermal0.12
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 739
Rwork0.266 6478
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)
13.109-0.00260.25581.57540.37331.34670.0102-0.144-1.10380.31250.0946-0.05010.21710.0757-0.10480.13160.0302-0.0030.0395-0.00940.4703-0.9701164.650617.5189
21.8528-0.29060.19611.4841-0.17740.92320.08070.6356-0.8901-0.2088-0.00420.25070.14530.0803-0.07650.08520.0087-0.03220.3078-0.41120.5767-3.8751161.379-7.1847
31.84440.48420.72892.14630.49061.3643-0.1112-0.31990.00270.51870.02640.134-0.1015-0.23510.08480.26030.06450.00510.0885-0.01740.0549-3.4732193.73528.7123
42.0294-0.04650.10981.68080.34541.9241-0.24130.08550.53980.06710.1371-0.1459-0.4860.16770.10420.286-0.0393-0.11890.07320.02150.18253.2234212.977413.4805
52.1452-0.17910.52441.8970.33282.0639-0.26981.05730.4518-0.57670.12850.0107-0.57410.31320.14140.4501-0.2421-0.09550.61650.20830.1440.435208.5877-17.2514
61.8865-0.25330.36342.709-0.01691.02370.00321.249-0.2784-0.8507-0.0009-0.0917-0.14710.5106-0.00230.4013-0.09560.03370.9566-0.23130.10673.409184.961-26.0698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2534 - 256
2X-RAY DIFFRACTION2BB3 - 2536 - 256
3X-RAY DIFFRACTION3CC4 - 2537 - 256
4X-RAY DIFFRACTION4DD4 - 2537 - 256
5X-RAY DIFFRACTION5EE3 - 2536 - 256
6X-RAY DIFFRACTION6FF4 - 2537 - 256

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