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- PDB-2ada: ATOMIC STRUCTURE OF ADENOSINE DEAMINASE COMPLEXED WITH A TRANSITI... -

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Basic information

Entry
Database: PDB / ID: 2ada
TitleATOMIC STRUCTURE OF ADENOSINE DEAMINASE COMPLEXED WITH A TRANSITION-STATE ANALOG: UNDERSTANDING CATALYSIS AND IMMUNODEFICIENCY MUTATIONS
ComponentsADENOSINE DEAMINASE
KeywordsHYDROLASE / AMINO / ZINC COFACTOR / BETA/ALPHA BARREL / TRANSITION-STATE INHIBITOR
Function / homology
Function and homology information


mature B cell apoptotic process / purine nucleotide salvage / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding ...mature B cell apoptotic process / purine nucleotide salvage / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of circadian sleep/wake cycle, non-REM sleep / negative regulation of mucus secretion / penile erection / purine nucleoside binding / positive regulation of germinal center formation / negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / histamine secretion / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / amide catabolic process / adenosine deaminase / hypoxanthine biosynthetic process / germinal center B cell differentiation / adenosine catabolic process / adenosine deaminase activity / hypoxanthine salvage / inhibition of non-skeletal tissue mineralization / deaminase activity / deoxyadenosine catabolic process / dAMP catabolic process / AMP catabolic process / adenosine metabolic process / positive regulation of T cell differentiation in thymus / dATP catabolic process / negative regulation of leukocyte migration / mucus secretion / GMP salvage / response to purine-containing compound / regulation of cell-cell adhesion mediated by integrin / embryonic digestive tract development / allantoin metabolic process / trophectodermal cell differentiation / IMP salvage / positive regulation of smooth muscle contraction / germinal center formation / Peyer's patch development / negative regulation of mature B cell apoptotic process / AMP salvage / regulation of T cell differentiation in thymus / anchoring junction / negative regulation of thymocyte apoptotic process / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / positive regulation of T cell differentiation / regulation of T cell differentiation / positive regulation of heart rate / lung alveolus development / leukocyte migration / positive regulation of T cell receptor signaling pathway / thymocyte apoptotic process / B cell proliferation / T cell differentiation / smooth muscle contraction / response to inorganic substance / response to vitamin E / positive regulation of calcium-mediated signaling / positive regulation of B cell proliferation / dendrite cytoplasm / T cell activation / liver development / placenta development / calcium-mediated signaling / lung development / negative regulation of inflammatory response / positive regulation of T cell activation / T cell differentiation in thymus / T cell receptor signaling pathway / in utero embryonic development / lysosome / response to hypoxia / cell adhesion / external side of plasma membrane / neuronal cell body / apoptotic process / negative regulation of apoptotic process / cell surface / extracellular space / zinc ion binding / membrane / plasma membrane / cytosol / cytoplasm
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-7,8-DIHYDRO PURINE NUCLEOSIDE / Adenosine deaminase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsWilson, D.K. / Quiocho, F.A.
Citation
Journal: Science / Year: 1991
Title: Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations.
Authors: Wilson, D.K. / Rudolph, F.B. / Quiocho, F.A.
#1: Journal: Nat.Struct.Biol. / Year: 1994
Title: Crystallographic Observation of a Trapped Tetrahedral Intermediate in a Metalloenzyme
Authors: Wilson, D.K. / Quiocho, F.A.
#2: Journal: Biochemistry / Year: 1993
Title: A Pre-Transition-State Mimic of an Enzyme: X-Ray Structure of Adenosine Deaminase with Bound 1-Deazaadenosine
Authors: Wilson, D.K. / Quiocho, F.A.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Refined 2.5 Angstroms Structure of the Murine Adenosine Deaminase at Ph 6.0
Authors: Sharff, A.J. / Wilson, D.K. / Chang, Z.
#4: Journal: J.Mol.Biol. / Year: 1988
Title: Preliminary X-Ray Analysis of Crystals of Murine Adenosine Deaminase
Authors: Wilson, D.K. / Rudolph, F.B. / Harrison, M.L. / Kellems, R.E. / Quiocho, F.A.
History
DepositionDec 2, 1994Processing site: BNL
SupersessionMar 31, 1995ID: 1ADA
Revision 1.0Mar 31, 1995Provider: 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_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

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Assembly

Deposited unit
A: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3813
Polymers40,0461
Non-polymers3362
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.360, 94.110, 72.930
Angle α, β, γ (deg.)90.00, 127.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADENOSINE DEAMINASE /


Mass: 40045.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P03958, 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-HPR / 6-HYDROXY-7,8-DIHYDRO PURINE NUCLEOSIDE


Mass: 270.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOMPND LIGAND IS FORMED IN ENZYME ACTIVE SITE FROM PURINE RIBOSIDE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal grow
*PLUS
pH: 4.2 / Method: vapor diffusion / Details: Wilson, D.K., (1988) J.Mol.Biol., 200, 613.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
250 mM1dropKCl
350 mMsodium citrate1drop
47.5 %PEG60001drop
515 %PEG60001reservoir

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Data collection

ReflectionNum. obs: 20445 / % possible obs: 93 % / Observed criterion σ(F): 3
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 72059 / Rmerge(I) obs: 0.0324

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→10 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.195 -
obs0.195 20445
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 20 58 2870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.003
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_deg1.366
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_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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