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- PDB-3km8: Crystal structuore of adenosine deaminase from mus musculus compl... -

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Basic information

Entry
Database: PDB / ID: 3km8
TitleCrystal structuore of adenosine deaminase from mus musculus complexed with 9-deazainosine
ComponentsAdenosine deaminase
KeywordsHYDROLASE / CYCLICAMIDINES / Metal-binding / Nucleotide metabolism
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
9-DEAZAINOSINE / Adenosine deaminase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFan, X. / Gao, Y.
CitationJournal: To be Published
Title: The Catalytic Mechanism of Adenosine Deaminase from Mouse: An Experimental and Theoretical Study
Authors: Wu, X. / Fan, X. / Gao, Y. / Su, X. / Zhang, H. / Wu, Y.
History
DepositionNov 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenosine deaminase
B: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6866
Polymers80,0212
Non-polymers6654
Water6,413356
1
A: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3433
Polymers40,0111
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3433
Polymers40,0111
Non-polymers3332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.337, 93.616, 85.416
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

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Components

#1: Protein Adenosine deaminase / / Adenosine aminohydrolase


Mass: 40010.543 Da / Num. of mol.: 2 / Mutation: E217Q, Y240E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ada / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P03958, adenosine deaminase
#2: Chemical ChemComp-9DI / 9-DEAZAINOSINE


Mass: 267.238 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N3O5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% PEG 2000 MME, 150mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 11, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→84.82 Å / Num. obs: 48057 / % possible obs: 90.8 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 3 / Redundancy: 9.53 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.28 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3 / Num. unique all: 5295 / % possible all: 84.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
REFMAC5.5.0102refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADD

1add


Resolution: 2→37.48 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.791 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22308 2433 5.1 %RANDOM
Rwork0.20199 ---
all0.2031 ---
obs0.2031 45618 90.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.619 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å20 Å21.12 Å2
2---1.31 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 40 356 5972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225744
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.9747778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.93324.667270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.782151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5211530
X-RAY DIFFRACTIONr_chiral_restr0.1940.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0214342
X-RAY DIFFRACTIONr_mcbond_it1.5271.53480
X-RAY DIFFRACTIONr_mcangle_it2.46925634
X-RAY DIFFRACTIONr_scbond_it4.24132264
X-RAY DIFFRACTIONr_scangle_it6.3774.52144
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 163 -
Rwork0.279 3129 -
obs-3129 84.37 %

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