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- PDB-1ezr: CRYSTAL STRUCTURE OF NUCLEOSIDE HYDROLASE FROM LEISHMANIA MAJOR -

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Basic information

Entry
Database: PDB / ID: 1ezr
TitleCRYSTAL STRUCTURE OF NUCLEOSIDE HYDROLASE FROM LEISHMANIA MAJOR
ComponentsNUCLEOSIDE HYDROLASE
KeywordsHYDROLASE / alpha/beta fold
Function / homology
Function and homology information


inosine nucleosidase / uridine nucleosidase / inosine nucleosidase activity / uridine nucleosidase activity / purine nucleosidase activity / purine-containing compound salvage / nucleotide metabolic process / calcium 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
Inosine-uridine preferring nucleoside hydrolase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsShi, W. / Schramm, V.L. / Almo, S.C.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Nucleoside hydrolase from Leishmania major. Cloning, expression, catalytic properties, transition state inhibitors, and the 2.5-a crystal structure.
Authors: Shi, W. / Schramm, V.L. / Almo, S.C.
History
DepositionMay 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_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: NUCLEOSIDE HYDROLASE
B: NUCLEOSIDE HYDROLASE
C: NUCLEOSIDE HYDROLASE
D: NUCLEOSIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,3878
Polymers137,2274
Non-polymers1604
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-86 kcal/mol
Surface area46120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.8, 79.2, 109.8
Angle α, β, γ (deg.)90.0, 91.6, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a tetramer in the asymmetric unit.

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Components

#1: Protein
NUCLEOSIDE HYDROLASE


Mass: 34306.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid: PMW172 / Production host: Escherichia coli (E. coli) / References: UniProt: P83851, purine nucleosidase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-15 mg/mlprotein1drop
2100 mMMES1reservoir
316 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. all: 41035 / Num. obs: 41035 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.45 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.306 / Num. unique all: 3273 / % possible all: 67.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 113835

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
X-GENdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / σ(F): 2 / σ(I): 1.4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1611 -random
Rwork0.203 ---
all0.205 41023 --
obs0.205 40410 98.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9352 0 4 100 9456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007
X-RAY DIFFRACTIONc_angle_deg1.254
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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