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- PDB-3mvi: Crystal structure of holo mADA at 1.6 A resolution -

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Basic information

Entry
Database: PDB / ID: 3mvi
TitleCrystal structure of holo mADA at 1.6 A resolution
ComponentsAdenosine deaminase
KeywordsHYDROLASE / ADENOSINE DEAMINASE
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
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
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsNiu, W. / Shu, Q. / Chen, Z. / Mathews, S. / Di Cera, E. / Frieden, C.
Citation
Journal: J.Phys.Chem.B / Year: 2010
Title: The role of Zn2+ on the structure and stability of murine adenosine deaminase.
Authors: Niu, W. / Shu, Q. / Chen, Z. / Mathews, S. / Di Cera, E. / Frieden, C.
#1: 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.
History
DepositionMay 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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
B: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7456
Polymers79,4302
Non-polymers3154
Water11,674648
1
A: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8733
Polymers39,7151
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8733
Polymers39,7151
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.670, 93.804, 88.048
Angle α, β, γ (deg.)90.00, 105.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenosine deaminase / / Adenosine aminohydrolase


Mass: 39715.188 Da / Num. of mol.: 2 / Fragment: UNP residues 4-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ada / Plasmid: PRC4 / Production host: Escherichia coli (E. coli) / References: UniProt: P03958, adenosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris_HCl, pH 8.5 and 25% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2007
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 92164 / Num. obs: 92164 / % possible obs: 95.9 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.2 / Num. unique all: 7626 / % possible all: 79.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPfrom CCP4phasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1a4m

1a4m


Resolution: 1.6→19.66 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.961 / SU ML: 0.067 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20487 4624 5 %RANDOM
Rwork0.1683 ---
obs0.17015 92137 95.94 %-
all-91215 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5584 0 14 648 6246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225722
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9687742
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4815696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10824.593270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.873151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.641530
X-RAY DIFFRACTIONr_chiral_restr0.0970.2842
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214336
X-RAY DIFFRACTIONr_mcbond_it0.7061.53482
X-RAY DIFFRACTIONr_mcangle_it1.30825638
X-RAY DIFFRACTIONr_scbond_it2.2832240
X-RAY DIFFRACTIONr_scangle_it3.8574.52104
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 259 -
Rwork0.285 5227 -
obs-5227 78.83 %

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