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- PDB-3g5i: Crystal Structure of the E.coli RihA pyrimidine nucleosidase boun... -

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Basic information

Entry
Database: PDB / ID: 3g5i
TitleCrystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor
ComponentsPyrimidine-specific ribonucleoside hydrolase rihA
KeywordsHYDROLASE / Open (alpha / beta) structure / Glycosidase
Function / homology
Function and homology information


ribosylpyrimidine nucleosidase activity / pyrimidine ribonucleoside catabolic process / Hydrolases; Glycosylases / uridine nucleosidase activity / purine nucleosidase activity / pyrimidine nucleobase metabolic process / nucleobase-containing small molecule interconversion / purine nucleoside catabolic process / protein homotetramerization / calcium ion binding ...ribosylpyrimidine nucleosidase activity / pyrimidine ribonucleoside catabolic process / Hydrolases; Glycosylases / uridine nucleosidase activity / purine nucleosidase activity / pyrimidine nucleobase metabolic process / nucleobase-containing small molecule interconversion / purine nucleoside catabolic process / protein homotetramerization / calcium ion binding / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Pyrimidine-specific ribonucleoside hydrolase RihA / 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
BETA-MERCAPTOETHANOL / Chem-DNB / Pyrimidine-specific ribonucleoside hydrolase RihA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGarau, G. / Muzzolini, L. / Tornaghi, P. / Degano, M.
Citation
Journal: Bmc Struct.Biol. / Year: 2010
Title: Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor.
Authors: Garau, G. / Muzzolini, L. / Tornaghi, P. / Degano, M.
#1: Journal: Biochemistry / Year: 2006
Title: New insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product
Authors: Muzzolini, L. / Versees, W. / Tornaghi, P. / Van Holsbeke, E. / Steyaert, J. / Degano, M.
#2: 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.
History
DepositionFeb 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 17, 2021Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyrimidine-specific ribonucleoside hydrolase rihA
B: Pyrimidine-specific ribonucleoside hydrolase rihA
C: Pyrimidine-specific ribonucleoside hydrolase rihA
D: Pyrimidine-specific ribonucleoside hydrolase rihA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,66213
Polymers135,4674
Non-polymers1,1969
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-75 kcal/mol
Surface area40960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.350, 82.910, 93.870
Angle α, β, γ (deg.)90.00, 112.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 56
2111B2 - 56
3111C2 - 56
4111D2 - 56
1211A86 - 218
2211B86 - 218
3211C86 - 218
4211D86 - 218
1311A232 - 302
2311B232 - 302
3311C232 - 302
4311D232 - 302
1411A306 - 312
2411B306 - 312
3411C306 - 312
4411D306 - 312
1511A58 - 75
2511B58 - 75
3511C58 - 75
4511D58 - 75

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Components

#1: Protein
Pyrimidine-specific ribonucleoside hydrolase rihA / RihA/YbeK pyrimidine nucleoside hydrolase / Cytidine/uridine-specific hydrolase


Mass: 33866.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ybeK / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P41409, ribosylpyrimidine nucleosidase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-DNB / (2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol / Diaminophenyl iminoribitol


Mass: 239.271 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H17N3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium Acetate, 25% PEG 4000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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 210 / Detector: CCD / Date: Apr 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 68457 / Num. obs: 68457 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 30.7 Å2 / Rsym value: 0.122 / Net I/σ(I): 8.12
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3 / Num. unique all: 4942 / Rsym value: 0.388 / % possible all: 95.4

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YOE

1yoe


Resolution: 2.1→37.5 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.733 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.265 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24093 3455 5 %RANDOM
Rwork0.20285 ---
all0.20477 65238 --
obs0.20477 65238 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.861 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å20 Å2-1.3 Å2
2--3.48 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9119 0 71 510 9700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0229406
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.98412853
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45951193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09224.758372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.378151503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8861544
X-RAY DIFFRACTIONr_chiral_restr0.1040.21533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027026
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.24589
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.26565
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0260.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3110.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4130.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8461.56148
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.29629705
X-RAY DIFFRACTIONr_scbond_it2.14133693
X-RAY DIFFRACTIONr_scangle_it3.284.53145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2126 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.070.05
2Btight positional0.080.05
3Ctight positional0.070.05
4Dtight positional0.060.05
1Atight thermal0.210.5
2Btight thermal0.190.5
3Ctight thermal0.190.5
4Dtight thermal0.180.5
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 265 -
Rwork0.254 4760 -
obs--97.36 %
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)
11.3028-0.06040.62770.692-0.49791.64580.08290.149-0.04130.01540.04110.0237-0.0131-0.0905-0.1241-0.09460.0170.0051-0.165-0.0118-0.077141.38030.442329.4039
21.60690.1688-0.6170.7934-0.30121.35810.1574-0.3708-0.01860.1857-0.0830.08030.06630.0641-0.07440.002-0.1370.0212-0.01820.0226-0.074241.1154-9.228668.3182
31.6923-0.0676-0.20380.83930.16911.92060.12080.2925-0.1811-0.1320.0325-0.10670.20410.1797-0.1533-0.04390.03930.005-0.0942-0.0672-0.027583.7775-7.929329.2437
41.77050.07990.58940.53210.50131.93570.158-0.364-0.10240.0410.0579-0.10270.0534-0.02-0.2159-0.0633-0.0819-0.0437-0.0610.0195-0.056483.54170.230668.7928
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 311
2X-RAY DIFFRACTION2B1 - 311
3X-RAY DIFFRACTION3C2 - 311
4X-RAY DIFFRACTION4D0 - 311

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