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- PDB-1a4m: ADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0 -

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Basic information

Entry
Database: PDB / ID: 1a4m
TitleADA STRUCTURE COMPLEXED WITH PURINE RIBOSIDE AT PH 7.0
ComponentsADENOSINE DEAMINASE
KeywordsHYDROLASE / ADENOSINE DEAMINASE / PURINE RIBOSIDE
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 / germinal center B cell differentiation / AMP catabolic process / adenosine deaminase activity / amide catabolic process / adenosine catabolic process / 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 / allantoin metabolic process / GMP salvage / 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 / liver development / calcium-mediated signaling / 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
6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE / Adenosine deaminase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, 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
DepositionJan 31, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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_auth_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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
B: ADENOSINE DEAMINASE
C: ADENOSINE DEAMINASE
D: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,20712
Polymers158,8614
Non-polymers1,3478
Water19,1861065
1
A: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0523
Polymers39,7151
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0523
Polymers39,7151
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0523
Polymers39,7151
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0523
Polymers39,7151
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.693, 93.644, 102.177
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADENOSINE DEAMINASE / ADA


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 / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PRH / 6-HYDROXY-1,6-DIHYDRO PURINE NUCLEOSIDE


Mass: 271.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N4O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1065 / 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: 2.6 Å3/Da / Density % sol: 58 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.2 mg/mlprotein1drop
25 mMDCF1drop
36.7 %PEG33501drop
433 mM1dropNaCl
533 mMHEPES1drop
620 %PEG33501reservoir
7100 mM1reservoirNaCl
8100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
X-PLOR3.85model building
X-PLOR3.85refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.85phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ADA

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
RfactorNum. reflection% reflectionSelection details
Rfree0.281 7677 10 %RANDOM
Rwork0.193 ---
obs0.193 76565 70.2 %-
Displacement parametersBiso mean: 16.96 Å2
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11168 0 76 1065 12309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.474
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.08
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.657
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 / Version: 3.85 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 77948
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.087
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.657

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