+Open data
-Basic information
Entry | Database: PDB / ID: 1a4m | ||||||
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Title | ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0 | ||||||
Components | ADENOSINE DEAMINASE | ||||||
Keywords | HYDROLASE / ADENOSINE DEAMINASE / PURINE RIBOSIDE | ||||||
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 / positive regulation of T cell receptor signaling pathway / leukocyte migration / 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 | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Wang, Z. / Quiocho, F.A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Complexes of adenosine deaminase with two potent inhibitors: X-ray structures in four independent molecules at pH of maximum activity. Authors: Wang, Z. / Quiocho, F.A. #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: J.Mol.Biol. / Year: 1992 Title: Refined 2.5 A Structure of Murine Adenosine Deaminase at Ph 6.0 Authors: Sharff, A.J. / Wilson, D.K. / Chang, Z. / Quiocho, F.A. #3: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a4m.cif.gz | 310 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a4m.ent.gz | 248.1 KB | Display | PDB format |
PDBx/mmJSON format | 1a4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a4m ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a4m | HTTPS FTP |
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-Related structure data
Related structure data | 1a4lC 2adaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39715.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): PRC4 / References: UniProt: P03958, adenosine deaminase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PRH / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 20% PEG 3350, 100 MM NACL, 100 MM HEPES PH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRROR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→10 Å / Num. obs: 83321 / % possible obs: 70.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.078 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.401 / % possible all: 47 |
Reflection | *PLUS Num. measured all: 415190 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 47 % / Rmerge(I) obs: 0.401 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ADA Resolution: 1.95→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 16.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.85 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 77948 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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