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- PDB-1krm: Crystal structure of bovine adenosine deaminase complexed with 6-... -

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Basic information

Entry
Database: PDB / ID: 1krm
TitleCrystal structure of bovine adenosine deaminase complexed with 6-hydroxyl-1,6-dihydropurine riboside
Componentsadenosine deaminase
KeywordsHYDROLASE / adenosine deaminase
Function / homology
Function and homology information


negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / nucleotide metabolic process ...negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / purine ribonucleoside monophosphate biosynthetic process / 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
6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE / Adenosine deaminase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKinoshita, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of bovine adenosine deaminase complexed with 6-hydroxy-1,6-dihydropurine riboside.
Authors: Kinoshita, T. / Nishio, N. / Nakanishi, I. / Sato, A. / Fujii, T.
History
DepositionJan 10, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 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_ref_seq_dif / 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_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_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_ref_seq_dif.details / _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: adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6633
Polymers40,3271
Non-polymers3372
Water8,827490
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.03, 80.03, 141.68
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein adenosine deaminase


Mass: 40326.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Strain: intestine / 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-PRH / 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE


Mass: 271.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 490 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: ammonium sulphate, PEG400, MES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Kinoshita, T., (1999) Acta Crystallogr.,Sect., D55, 2031.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0-2.2 Mammonium sulfate1reservoir
22 %(v/v)PEG4001reservoir
30.1 MHEPES1reservoirpH7.5
420 mg/mlprotein1drop
550 mMTris-HCl1droppH7.5
610 mMpurine riboside1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 12, 1999 / Details: monochromater
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 16308 / Num. obs: 15982 / % possible obs: 75.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rsym value: 0.117
Reflection shellResolution: 2.5→2.73 Å / Redundancy: 6.4 % / Rsym value: 0.185
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 16108 / % possible obs: 99.2 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 594 -random
Rwork0.196 ---
obs0.196 11304 75.4 %-
all-11898 --
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 20 490 3298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d4.1
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
LS refinement shellResolution: 2.5→2.6 Å / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.286
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.83

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