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- PDB-1q8f: Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK -

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Basic information

Entry
Database: PDB / ID: 1q8f
TitleCrystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK
ComponentsPyrimidine nucleoside hydrolase
KeywordsHYDROLASE / open alpha-beta structure / NH-fold
Function / homology
Function and homology information


ribosylpyrimidine nucleosidase / pyrimidine ribonucleoside catabolic process / uridine nucleosidase activity / purine nucleosidase activity / pyrimidine nucleobase metabolic process / purine nucleoside catabolic process / protein homotetramerization / calcium ion binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Pyrimidine-specific ribonucleoside hydrolase RihB / Inosine/uridine-preferring nucleoside hydrolase, conserved site / Inosine-uridine preferring nucleoside hydrolase family signature. / Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Pyrimidine-specific ribonucleoside hydrolase RihB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGiabbai, B. / Degano, M.
Citation
Journal: STRUCTURE / Year: 2004
Title: Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy.
Authors: Giabbai, B. / Degano, M.
#1: Journal: Biochemistry / Year: 1996
Title: Three-dimensional structure of the Inosine-Uridine Nucleoside N-ribohydrolase from Crithidia fasciculata
Authors: Degano, M. / Gopaul, D.N. / Scapin, G. / Schramm, V.L. / Sacchettini, J.C.
#2: Journal: Biochemistry / Year: 1998
Title: Trypanosomal nucleoside hydrolase. A novel mechanism from the structure with a transition-state inhibitor
Authors: Degano, M. / Almo, S.C. / Sacchettini, J.C. / Schramm, V.L.
#3: Journal: J.Mol.Biol. / Year: 2001
Title: Structure and function of a novel purine specific nucleoside hydrolase from Trypanosoma vivax
Authors: Versees, W. / Decanniere, K. / Pelle, R. / Depoorter, J. / Brosens, E. / Parkin, D.W. / Steyaert, J.
History
DepositionAug 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 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 / 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_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_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_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: Pyrimidine nucleoside hydrolase
B: Pyrimidine nucleoside hydrolase
C: Pyrimidine nucleoside hydrolase
D: Pyrimidine nucleoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,68124
Polymers135,0474
Non-polymers1,63420
Water19,0061055
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-105 kcal/mol
Surface area39200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.808, 85.707, 90.678
Angle α, β, γ (deg.)112.95, 101.95, 85.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
12A
22B
32C
42D
52A
62B
72C
82D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSPROPRO5AA3 - 903 - 90
211LYSLYSPROPRO5BB3 - 903 - 90
311LYSLYSPROPRO5CC3 - 903 - 90
411LYSLYSPROPRO5DD3 - 903 - 90
521GLUGLUTHRTHR5AA100 - 223100 - 223
621GLUGLUTHRTHR5BB100 - 223100 - 223
721GLUGLUTHRTHR5CC100 - 223100 - 223
821GLUGLUTHRTHR5DD100 - 223100 - 223
931GLYGLYILEILE5AA236 - 310236 - 310
1031GLYGLYILEILE5BB236 - 310236 - 310
1131GLYGLYILEILE5CC236 - 310236 - 310
1231GLYGLYILEILE5DD236 - 310236 - 310
112VALVALALAALA6AA91 - 9991 - 99
212VALVALALAALA6BB91 - 9991 - 99
312VALVALALAALA6CC91 - 9991 - 99
412VALVALALAALA6DD91 - 9991 - 99
522LEULEUGLYGLY6AA224 - 235224 - 235
622LEULEUGLYGLY6BB224 - 235224 - 235
722LEULEUGLYGLY6CC224 - 235224 - 235
822LEULEUGLYGLY6DD224 - 235224 - 235

NCS ensembles :
ID
1
2
DetailsThe biologically active tetramer is contained in the crystal asymmetric unit

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Components

#1: Protein
Pyrimidine nucleoside hydrolase / Pyrimidine nucleosidase / CU-NH / Hypothetical protein yeiK


Mass: 33761.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YEIK / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33022, ribosylpyrimidine nucleosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1055 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEGMME 3350, methanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 4, 2003 / Details: Mirror
RadiationMonochromator: Diamond crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.7→81.6 Å / Num. obs: 122468 / % possible obs: 91.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.046 / Net I/σ(I): 9.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3 / Num. unique all: 12529 / Rsym value: 0.221 / % possible all: 63.8

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1MAS

1mas


Resolution: 1.7→43.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.685 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.16989 1247 1 %RANDOM
Rwork0.15331 ---
all0.1534 121220 --
obs0.15348 121220 91.53 %-
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: 15.208 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.51 Å2-0.28 Å2
2---0.32 Å20.18 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9260 0 100 1055 10415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229520
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.97412940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85551228
X-RAY DIFFRACTIONr_chiral_restr0.0930.21508
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027100
X-RAY DIFFRACTIONr_nbd_refined0.20.24938
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2831
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.237
X-RAY DIFFRACTIONr_mcbond_it0.5661.56112
X-RAY DIFFRACTIONr_mcangle_it1.01129916
X-RAY DIFFRACTIONr_scbond_it2.00333408
X-RAY DIFFRACTIONr_scangle_it3.3364.53024
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2147medium positional0.190.5
12B2147medium positional0.180.5
13C2147medium positional0.190.5
14D2147medium positional0.190.5
21A168loose positional0.625
22B168loose positional0.55
23C168loose positional0.585
24D168loose positional0.665
11A2147medium thermal0.782
12B2147medium thermal1.892
13C2147medium thermal1.032
14D2147medium thermal1.412
21A168loose thermal1.8110
22B168loose thermal4.5910
23C168loose thermal1.5310
24D168loose thermal3.5610
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.182 52
Rwork0.185 5712
obs-5712
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)
10.1087-0.00250.07830.1188-0.0820.5059-0.0371-0.00140.00480.0350.0401-0.0047-0.1128-0.0295-0.0030.0540.0072-0.00440.02350.01030.0339-3.46520.5165-20.256
20.3452-0.27080.01780.6695-0.17160.4176-0.1076-0.10440.0360.18580.1101-0.0576-0.2026-0.0748-0.00250.150.0568-0.02970.0535-0.03150.01881.32321.679519.3808
30.239-0.0265-0.04520.2161-0.02480.1492-0.02520.0449-0.0246-0.02360.00520.0065-0.005-0.03760.020.0123-0.02020.01140.0465-0.01180.0407-7.7206-21.871-17.3751
40.1147-0.02520.06850.08930.00120.2483-0.0274-0.0182-0.02010.00220.0133-0.0183-0.0144-0.01520.01410.0035-0.0040.00870.04290.01990.04519.651-20.33618.4653
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 3103 - 310
2X-RAY DIFFRACTION2BB3 - 3103 - 310
3X-RAY DIFFRACTION3CC3 - 3103 - 310
4X-RAY DIFFRACTION4DD3 - 3103 - 310

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