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- PDB-1mas: PURINE NUCLEOSIDE HYDROLASE -

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Basic information

Entry
Database: PDB / ID: 1mas
TitlePURINE NUCLEOSIDE HYDROLASE
ComponentsINOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
KeywordsHYDROLASE / PURINE NUCLEOSIDE HYDROLASE / PURINE NUCLEOSIDASE / IU-NH
Function / homology
Function and homology information


inosine nucleosidase / uridine nucleosidase / inosine nucleosidase activity / uridine nucleosidase activity / purine nucleoside catabolic process / nucleotide metabolic process / metal ion binding / cytosol
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
: / Inosine-uridine preferring nucleoside hydrolase
Similarity search - Component
Biological speciesCrithidia fasciculata (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsDegano, M. / Gopaul, D.N. / Scapin, G. / Schramm, V.L. / Sacchettini, J.C.
Citation
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.
#1: Journal: Biochemistry / Year: 1996
Title: Inosine-Uridine Nucleoside Hydrolase from Crithidia Fasciculata. Genetic Characterization, Crystallization, and Identification of Histidine 241 as a Catalytic Site Residue
Authors: Gopaul, D.N. / Meyer, S.L. / Degano, M. / Sacchettini, J.C. / Schramm, V.L.
#2: Journal: Biochemistry / Year: 1991
Title: Transition-State Analysis of Nucleoside Hydrolase from Crithidia Fasciculata
Authors: Horenstein, B.A. / Parkin, D.W. / Estupinan, B. / Schramm, V.L.
#3: Journal: J.Biol.Chem. / Year: 1991
Title: Nucleoside Hydrolase from Crithidia Fasciculata
Authors: Parkin, D.W. / Horenstein, B.A. / Abdulah, D.R. / Estupinan, B. / Schramm, V.L.
History
DepositionDec 18, 1995Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4914
Polymers68,4132
Non-polymers782
Water1,31573
1
A: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
B: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
hetero molecules

A: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
B: INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,9828
Polymers136,8264
Non-polymers1564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)63.840, 131.530, 90.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3301, 0.943796, 0.016835), (0.943851, 0.329761, 0.020081), (0.0134, 0.022518, -0.999657)
Vector: -0.14923, -1.24879, 59.80751)

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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.: 2 / 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
134 mg/mlprotein1drop
210 mMphosphate1drop
310 mMglycine1drop
4100 mMpotassium citrate1reservoir
58 %PEG40001reservoir
60.05 %sodium azide1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 24, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. obs: 25989 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.071
Reflection
*PLUS
Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
XENGENV. 2.1data reduction
X-PLORphasing
RefinementResolution: 2.5→99 Å / σ(F): 2
Details: TORSION ANGLES NOT RESTRAINED. MEAN B VALUE IS 28.07 ANGSTROMS**. X-PLOR ALSO WAS USED. THE MOLECULE DENOTED BY CHAIN IDENTIFIER B SUFFERS A HIGHER DEGREE OF DISORDER, AS JUDGED FROM THE ...Details: TORSION ANGLES NOT RESTRAINED. MEAN B VALUE IS 28.07 ANGSTROMS**. X-PLOR ALSO WAS USED. THE MOLECULE DENOTED BY CHAIN IDENTIFIER B SUFFERS A HIGHER DEGREE OF DISORDER, AS JUDGED FROM THE TEMPERATURE FACTORS THAT ARE CONSIDERABLY HIGHER.
RfactorNum. reflection% reflection
Rwork0.17 --
obs-23135 89.1 %
Refinement stepCycle: LAST / Resolution: 2.5→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 2 73 4693
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0161
X-RAY DIFFRACTIONt_angle_deg2.029
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.51

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