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- PDB-2mas: PURINE NUCLEOSIDE HYDROLASE WITH A TRANSITION STATE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 2mas
TitlePURINE NUCLEOSIDE HYDROLASE WITH A TRANSITION STATE INHIBITOR
ComponentsINOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
KeywordsHYDROLASE / PURINE NUCLEOSIDE HYDROLASE / INOSINE / URIDINE / IU-NH / PURINE NUCLEOSIDASE
Function / homology
Function and homology information


inosine nucleosidase / uridine nucleosidase / inosine nucleosidase activity / uridine nucleosidase activity / organonitrogen compound metabolic process / nucleotide metabolic process / metal ion binding
Similarity search - Function
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
Chem-PIR / Inosine-uridine preferring nucleoside hydrolase
Similarity search - Component
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDegano, M. / Schramm, V.L. / Sacchettini, J.C.
Citation
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.
#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.
History
DepositionOct 17, 1996Processing site: BNL
Revision 1.0Aug 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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_conn.ptnr2_label_seq_id / _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: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
B: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
C: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
D: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,88312
Polymers136,8264
Non-polymers1,0578
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-88 kcal/mol
Surface area43250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.630, 159.760, 206.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.95603, -0.25681, 0.1416), (-0.25695, -0.96626, -0.01761), (0.14135, -0.01955, -0.98977)0.64351, 65.85996, 115.14281
2given(-0.97926, 0.02353, -0.20121), (0.02047, -0.97665, -0.21386), (-0.20155, -0.21355, 0.95592)196.5239, 52.78437, 26.09237
3given(-0.96656, 0.25384, 0.03639), (0.25502, 0.93664, 0.24015), (0.02687, 0.2414, -0.97005)174.86868, -37.66309, 118.98824

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Components

#1: Protein
INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE / PURINE NUCLEOSIDE HYDROLASE / INOSINE-URIDINE NUCLEOSIDASE / IU-NH


Mass: 34206.480 Da / Num. of mol.: 4 / Mutation: P2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crithidia fasciculata (eukaryote) / Gene: IU-NH FROM C. FASCICULATA / Plasmid: PET3D-IUNH / Gene (production host): IU-NH FROM C. FASCICULATA / Production host: Escherichia coli (E. coli) / References: UniProt: Q27546, purine nucleosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PIR / 2-(4-AMINO-PHENYL)-5-HYDROXYMETHYL-PYRROLIDINE-3,4-DIOL


Mass: 224.256 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H16N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.58 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.5 / Details: 1.8 M AMMONIUM SULFATE, 3% ISOPROPANOL, pH 7.5
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
134 mg/mlenzyme1drop
21.0 mMsubunits1drop
30.25 mMtetramer1drop
410 mMtriethanolamine1drop
54 mMinhibitor1drop
61.8 Mammonium sulfate1reservoir
73 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 16, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionLowest resolution: 2.3 Å / Num. obs: 73166 / % possible obs: 80.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.31
Reflection shellResolution: 2.3→2.5 Å / Mean I/σ(I) obs: 2.2 / % possible all: 75.1
Reflection
*PLUS
Highest resolution: 2.3 Å
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SAINTdata reduction
SAINTdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNLIGANDED IU-NH (PDB CODE 1MAS), WATERS AND IONS REMOVED

1mas


Highest resolution: 2.3 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 6118 7 %SHELLS
Rwork0.205 ---
obs0.205 73166 80.8 %-
Displacement parametersBiso mean: 29.1 Å2
Refine analyzeLuzzati coordinate error free: 0.35 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9560 0 72 158 9790
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.461.5
X-RAY DIFFRACTIONx_mcangle_it2.612
X-RAY DIFFRACTIONx_scbond_it2.462
X-RAY DIFFRACTIONx_scangle_it2.612.5
Refine LS restraints NCSRms dev Biso : 1.5 Å2 / Rms dev position: 0.04 Å / Weight Biso : 3 / Weight position: 500
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.362 644 6.7 %
Rwork0.323 5906 -
obs--75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor obs: 0.323

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