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- PDB-1add: A PRE-TRANSITION STATE MIMIC OF AN ENZYME: X-RAY STRUCTURE OF ADE... -

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Basic information

Entry
Database: PDB / ID: 1add
TitleA PRE-TRANSITION STATE MIMIC OF AN ENZYME: X-RAY STRUCTURE OF ADENOSINE DEAMINASE WITH BOUND 1-DEAZA-ADENOSINE AND ZINC-ACTIVATED WATER
ComponentsADENOSINE DEAMINASE
KeywordsHYDROLASE(ACTING IN CYCLICAMIDINES)
Function / homology
Function and homology information


mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of mucus secretion / penile erection / positive regulation of germinal center formation / 2'-deoxyadenosine deaminase activity / negative regulation of adenosine receptor signaling pathway ...mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / Purine salvage / Ribavirin ADME / negative regulation of mucus secretion / penile erection / positive regulation of germinal center formation / 2'-deoxyadenosine deaminase activity / negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / hypoxanthine biosynthetic process / deoxyadenosine catabolic process / dAMP catabolic process / inhibition of non-skeletal tissue mineralization / inosine biosynthetic process / adenosine deaminase / amide catabolic process / adenosine deaminase activity / AMP catabolic process / adenosine catabolic process / germinal center B cell differentiation / positive regulation of T cell differentiation in thymus / dATP catabolic process / negative regulation of leukocyte migration / mucus secretion / positive regulation of smooth muscle contraction / regulation of cell-cell adhesion mediated by integrin / response to purine-containing compound / GMP salvage / allantoin metabolic process / embryonic digestive tract development / trophectodermal cell differentiation / IMP salvage / Peyer's patch development / negative regulation of mature B cell apoptotic process / AMP salvage / negative regulation of thymocyte apoptotic process / germinal center formation / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / anchoring junction / regulation of T cell differentiation / positive regulation of T cell differentiation / leukocyte migration / lung alveolus development / thymocyte apoptotic process / positive regulation of T cell receptor signaling pathway / B cell proliferation / smooth muscle contraction / T cell differentiation / positive regulation of heart rate / positive regulation of B cell proliferation / positive regulation of calcium-mediated signaling / lung development / T cell activation / placenta development / calcium-mediated signaling / liver development / positive regulation of T cell activation / negative regulation of inflammatory response / T cell differentiation in thymus / T cell receptor signaling pathway / in utero embryonic development / response to hypoxia / lysosome / cell adhesion / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / zinc ion binding / cytoplasm / 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
1-DEAZA-ADENOSINE / 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: Biochemistry / Year: 1993
Title: A pre-transition-state mimic of an enzyme: X-ray structure of adenosine deaminase with bound 1-deazaadenosine and zinc-activated water.
Authors: Wilson, D.K. / Quiocho, F.A.
#1: Journal: Science / Year: 1991
Title: Atomic Structure of Adenosine Deaminase Complexed with a Transition Analog: Understanding Catalysis and Immunodeficiency Mutations
Authors: Wilson, D.K. / Rudolph, F.B. / Quiocho, F.A.
#2: Journal: J.Mol.Biol. / Year: 1988
Title: Preliminary X-Ray Analysis of Murine Adenosine Deaminase
Authors: Wilson, D.K. / Rudolph, F.B. / Harrison, M.L. / Kellems, R.E. / Quiocho, F.A.
History
DepositionDec 22, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0473
Polymers39,7151
Non-polymers3322
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.390, 94.280, 73.020
Angle α, β, γ (deg.)90.00, 127.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADENOSINE DEAMINASE


Mass: 39715.188 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-1DA / 1-DEAZA-ADENOSINE


Mass: 266.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.54 Å3/Da / Density % sol: 65.25 %
Crystal grow
*PLUS
pH: 4.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mLADA1drop
20.05 mMDAA1drop
33 %PEG60001drop
450 mMcitrate1drop
510.5 %PEG60001reservoir
650 mMcitrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 12 Å / Num. obs: 20925 / Num. measured all: 63922 / Rmerge(I) obs: 0.067

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.181 / Rfactor obs: 0.181 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 20 110 2922
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.71
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 12 Å / Num. reflection obs: 20925 / σ(F): 1 / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.71

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