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- PDB-2z7g: Crystal structure of adenosine deaminase ligated with EHNA -

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Basic information

Entry
Database: PDB / ID: 2z7g
TitleCrystal structure of adenosine deaminase ligated with EHNA
ComponentsAdenosine deaminase
KeywordsHYDROLASE / beta barrel / protein-inhibitor complex / Acetylation / Nucleotide metabolism / Pharmaceutical / Polymorphism
Function / homology
Function and homology information


negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / inosine biosynthetic process / adenosine deaminase / 2'-deoxyadenosine deaminase activity / hypoxanthine salvage / adenosine catabolic process / purine ribonucleoside monophosphate biosynthetic process / adenosine deaminase activity / nucleotide metabolic process ...negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / inosine biosynthetic process / adenosine deaminase / 2'-deoxyadenosine deaminase activity / hypoxanthine salvage / adenosine catabolic process / purine ribonucleoside monophosphate biosynthetic process / adenosine deaminase activity / nucleotide metabolic process / anchoring junction / T cell activation / lysosome / cell adhesion / external side of plasma membrane / zinc ion binding / cytosol
Similarity search - Function
Adenosine deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
(2S,3R)-3-(6-amino-9H-purin-9-yl)nonan-2-ol / Adenosine deaminase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.52 Å
AuthorsKinoshita, T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Conformational change of adenosine deaminase during ligand-exchange in a crystal
Authors: Kinoshita, T. / Tada, T. / Nakanishi, I.
History
DepositionAug 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6843
Polymers40,3421
Non-polymers3432
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 77.100, 135.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Adenosine deaminase / EHNA; synthetic compound / Adenosine aminohydrolase


Mass: 40341.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P56658, adenosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EH9 / (2S,3R)-3-(6-amino-9H-purin-9-yl)nonan-2-ol / Erythro-9-[3-(2-hydroxynonyl)] adenine / EHNA


Mass: 277.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H23N5O / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ADA_BOVIN. GLN 196, THR 243, AND ARG 349 ARE ...THE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ADA_BOVIN. GLN 196, THR 243, AND ARG 349 ARE VARIANTS OF ADA_BOVIN.

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2M Ammonium sulfate, 2% MPD, 0.1M MES buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 31, 2007 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.52→67.03 Å / Num. all: 14440 / Num. obs: 13675 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.4
Reflection shellResolution: 2.52→2.75 Å / Rmerge(I) obs: 0.167 / Mean I/σ(I) obs: 3.7 / % possible all: 94.5

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Processing

Software
NameClassification
CrystalCleardata collection
MOLREPphasing
CNXrefinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1KRM

1krm


Resolution: 2.52→67.03 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 719 -random
Rwork0.207 ---
all0.22 13675 --
obs0.21 12956 5.3 %-
Refinement stepCycle: LAST / Resolution: 2.52→67.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2789 0 21 119 2929
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.52→2.57 Å / Rfactor Rfree: 0.331 / Rfactor Rwork: 0.251

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