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- PDB-3b9x: Crystal structure of the E. coli pyrimidine nucleoside hydrolase ... -

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Basic information

Entry
Database: PDB / ID: 3b9x
TitleCrystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine
ComponentsPyrimidine-specific ribonucleoside hydrolase rihB
KeywordsHYDROLASE / Open (alpha / beta) structure / NH-fold / enzyme-substrate complex / protein-nucleoside complex / Glycosidase / Metal-binding
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
INOSINE / Pyrimidine-specific ribonucleoside hydrolase RihB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIovane, E. / Degano, M.
Citation
Journal: Biochemistry / Year: 2008
Title: Structural basis for substrate specificity in group I nucleoside hydrolases
Authors: Iovane, E. / Giabbai, B. / Muzzolini, L. / Matafora, V. / Fornili, A. / Minici, C. / Giannese, F. / Degano, M.
#1: 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.
#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.
History
DepositionNov 7, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 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_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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_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-specific ribonucleoside hydrolase rihB
B: Pyrimidine-specific ribonucleoside hydrolase rihB
C: Pyrimidine-specific ribonucleoside hydrolase rihB
D: Pyrimidine-specific ribonucleoside hydrolase rihB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,12913
Polymers143,7334
Non-polymers1,3969
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-97 kcal/mol
Surface area40060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.112, 82.406, 90.163
Angle α, β, γ (deg.)67.90, 79.59, 89.65
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
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSVALVAL1AA3 - 7723 - 97
21LYSLYSVALVAL1BB3 - 7723 - 97
31LYSLYSVALVAL1CC3 - 7723 - 97
41LYSLYSVALVAL1DD3 - 7723 - 97
52HISHISILEILE1AA239 - 310259 - 330
62HISHISILEILE1BB239 - 310259 - 330
72HISHISTYRTYR1CC239 - 309259 - 329
82HISHISILEILE1DD239 - 310259 - 330
93ASNASNVALVAL4AA221 - 238241 - 258
103ASNASNVALVAL4BB221 - 238241 - 258
113PROPROVALVAL4CC237 - 238257 - 258
123ASNASNVALVAL4DD221 - 238241 - 258
134VALVALMETMET1AA201 - 220221 - 240
144VALVALMETMET1BB201 - 220221 - 240
154VALVALASPASP1CC201 - 218221 - 238
164VALVALMETMET1DD201 - 220221 - 240
175ALAALASERSER6AA78 - 10198 - 121
185ALAALASERSER6BB78 - 10198 - 121
195ALAALASERSER6CC78 - 10198 - 121
205ALAALASERSER6DD78 - 10198 - 121
216THRTHRALAALA1AA102 - 174122 - 194
226THRTHRALAALA1BB102 - 174122 - 194
236THRTHRALAALA1CC102 - 174122 - 194
246THRTHRALAALA1DD102 - 174122 - 194
257VALVALPROPRO1AA176 - 199196 - 219
267VALVALPROPRO1BB176 - 199196 - 219
277VALVALPROPRO1CC176 - 199196 - 219
287VALVALPROPRO1DD176 - 199196 - 219

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Components

#1: Protein
Pyrimidine-specific ribonucleoside hydrolase rihB / Cytidine/uridine-specific hydrolase


Mass: 35933.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rihB, 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-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N4O5
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS FEEL THAT THE CONFLICT REPRESENTS A MUTATION IN THE DEPOSITED SEQUENCE.

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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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M NaCl, 24% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 13, 2007 / Details: Osmic
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 50148 / Num. obs: 50148 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.095 / Net I/σ(I): 18.7
Reflection shellResolution: 2.3→2.45 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 8.9 / Num. unique all: 5843 / Rsym value: 0.235 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q8F

1q8f


Resolution: 2.3→81.92 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.875 / SU B: 8.481 / SU ML: 0.205 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.447 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1560 3.1 %RANDOM
Rwork0.201 ---
obs0.203 48587 95.58 %-
all-48587 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.98 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.54 Å20.51 Å2
2---0.23 Å20.02 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.3→81.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9030 0 91 331 9452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229313
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.98912690
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36851198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08225.221362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.107151521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0261541
X-RAY DIFFRACTIONr_chiral_restr0.0920.21494
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026947
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.24426
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.26437
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2415
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.130.26
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2590.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.51656160
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.38969696
X-RAY DIFFRACTIONr_scbond_it3.75963585
X-RAY DIFFRACTIONr_scangle_it4.7287.52993
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
1A1940tight positional0.060.05
2B1940tight positional0.060.05
3C1940tight positional0.060.05
4D1940tight positional0.050.05
1A14medium positional0.320.2
2B14medium positional0.20.2
3C14medium positional0.320.2
4D14medium positional0.130.2
1A132loose positional0.370.2
2B132loose positional0.310.2
3C132loose positional0.40.2
4D132loose positional0.410.2
1A1940tight thermal0.20.5
2B1940tight thermal0.180.5
3C1940tight thermal0.210.5
4D1940tight thermal0.180.5
1A14medium thermal3.772
2B14medium thermal1.342
3C14medium thermal1.762
4D14medium thermal1.222
1A132loose thermal11.3325
2B132loose thermal5.8525
3C132loose thermal12.3325
4D132loose thermal5.125
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 90 -
Rwork0.248 3522 -
obs--92.03 %

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