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- PDB-1fkx: MURINE ADENOSINE DEAMINASE (D296A) -

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Basic information

Entry
Database: PDB / ID: 1fkx
TitleMURINE ADENOSINE DEAMINASE (D296A)
ComponentsADENOSINE DEAMINASE
KeywordsAMINOHYDROLASE / ZINC COFACTOR / TIM BARREL
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 / negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen ...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 / negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / amide catabolic process / hypoxanthine biosynthetic process / germinal center B cell differentiation / 2'-deoxyadenosine deaminase activity / inosine biosynthetic process / inhibition of non-skeletal tissue mineralization / deoxyadenosine catabolic process / dAMP catabolic process / adenosine deaminase / adenosine catabolic process / AMP catabolic process / positive regulation of T cell differentiation in thymus / dATP catabolic process / negative regulation of leukocyte migration / mucus secretion / adenosine deaminase activity / regulation of cell-cell adhesion mediated by integrin / allantoin metabolic process / embryonic digestive tract development / GMP salvage / IMP salvage / trophectodermal cell differentiation / response to purine-containing compound / positive regulation of smooth muscle contraction / 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 / thymocyte apoptotic process / lung alveolus development / positive regulation of T cell receptor signaling pathway / B cell proliferation / T cell differentiation / smooth muscle contraction / positive regulation of heart rate / positive regulation of B cell proliferation / positive regulation of calcium-mediated signaling / liver development / T cell activation / placenta development / lung development / calcium-mediated signaling / negative regulation of inflammatory response / positive regulation of T cell activation / T cell receptor signaling pathway / T cell differentiation in thymus / in utero embryonic development / lysosome / response to hypoxia / cell adhesion / external side of plasma membrane / apoptotic process / negative regulation of apoptotic process / zinc ion binding / 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-1,6-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: Biochemistry / Year: 1996
Title: Probing the functional role of two conserved active site aspartates in mouse adenosine deaminase.
Authors: Sideraki, V. / Mohamedali, K.A. / Wilson, D.K. / Chang, Z. / Kellems, R.E. / Quiocho, F.A. / Rudolph, F.B.
#1: 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.
#2: 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.
History
DepositionFeb 29, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_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_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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)40,0083
Polymers39,6711
Non-polymers3372
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.710, 94.070, 73.080
Angle α, β, γ (deg.)90.00, 127.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADENOSINE DEAMINASE


Mass: 39671.180 Da / Num. of mol.: 1 / Mutation: D296A
Source method: isolated from a genetically manipulated source
Details: LIGANDED TO ZINC, 6(R)-HYDROXY-1,6-DIHYDROPURINE RIBOSIDE
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-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.: 60 / 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
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

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 2, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15662 / Observed criterion σ(I): 1 / Redundancy: 1.6 % / Rmerge(I) obs: 0.0422
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. measured all: 25228 / Rmerge(I) obs: 0.042

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
SDMSDETECTOR SYSTEM (NIELSEN)data reduction
X-PLORphasing
RefinementResolution: 2.4→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.158 -
obs0.158 13684
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 20 60 2870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg
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
Rfactor obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.68

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