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- PDB-7rtg: Crystal Structure of the Human Adenosine Deaminase 1 -

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Basic information

Entry
Database: PDB / ID: 7rtg
TitleCrystal Structure of the Human Adenosine Deaminase 1
ComponentsAdenosine deaminase
KeywordsHYDROLASE / adenosine deaminase / zinc binding enzyme / holoenzyme
Function / homology
Function and homology information


purine nucleotide salvage / Defective ADA disrupts (deoxy)adenosine deamination / mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / negative regulation of mucus secretion / penile erection / positive regulation of germinal center formation / negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process ...purine nucleotide salvage / Defective ADA disrupts (deoxy)adenosine deamination / mature B cell apoptotic process / xanthine biosynthetic process / negative regulation of penile erection / negative regulation of mucus secretion / penile erection / positive regulation of germinal center formation / negative regulation of adenosine receptor signaling pathway / inosine biosynthetic process / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / amide catabolic process / adenosine deaminase / germinal center B cell differentiation / adenosine catabolic process / purine-containing compound salvage / deaminase activity / adenosine deaminase activity / hypoxanthine salvage / deoxyadenosine catabolic process / dAMP catabolic process / adenosine metabolic process / AMP catabolic process / positive regulation of T cell differentiation in thymus / dATP catabolic process / negative regulation of leukocyte migration / mucus secretion / Ribavirin ADME / regulation of cell-cell adhesion mediated by integrin / response to purine-containing compound / embryonic digestive tract development / allantoin metabolic process / trophectodermal cell differentiation / GMP salvage / Purine salvage / positive regulation of smooth muscle contraction / Peyer's patch development / germinal center formation / negative regulation of mature B cell apoptotic process / AMP salvage / negative regulation of thymocyte apoptotic process / anchoring junction / positive regulation of alpha-beta T cell differentiation / alpha-beta T cell differentiation / positive regulation of heart rate / leukocyte migration / lung alveolus development / positive regulation of T cell receptor signaling pathway / thymocyte apoptotic process / B cell proliferation / smooth muscle contraction / : / positive regulation of calcium-mediated signaling / positive regulation of B cell proliferation / T cell activation / xenobiotic metabolic process / liver development / calcium-mediated signaling / placenta development / negative regulation of inflammatory response / T cell differentiation in thymus / T cell receptor signaling pathway / lysosome / response to hypoxia / cell adhesion / external side of plasma membrane / cell surface / zinc ion binding / membrane / plasma membrane / 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 hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.591 Å
AuthorsMa, M.T. / Lieberman, R.L. / Blazeck, J. / Jennings, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateNA United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Catalytically active holo Homo sapiens adenosine deaminase I adopts a closed conformation.
Authors: Ma, M.T. / Jennings, M.R. / Blazeck, J. / Lieberman, R.L.
History
DepositionAug 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)83,7564
Polymers83,6252
Non-polymers1312
Water43224
1
A: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8782
Polymers41,8121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8782
Polymers41,8121
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.910, 49.519, 89.085
Angle α, β, γ (deg.)90.000, 96.180, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-512-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 109 or resid 111 through 137 or resid 139 through 353))
21(chain B and (resid 5 through 109 or resid 111 through 137 or resid 139 through 353))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROASNASN(chain A and (resid 5 through 109 or resid 111 through 137 or resid 139 through 353))AA5 - 1095 - 109
12LYSLYSLEULEU(chain A and (resid 5 through 109 or resid 111 through 137 or resid 139 through 353))AA111 - 137111 - 137
13GLUGLUMETMET(chain A and (resid 5 through 109 or resid 111 through 137 or resid 139 through 353))AA139 - 353139 - 353
21PROPROASNASN(chain B and (resid 5 through 109 or resid 111 through 137 or resid 139 through 353))BB5 - 1095 - 109
22LYSLYSLEULEU(chain B and (resid 5 through 109 or resid 111 through 137 or resid 139 through 353))BB111 - 137111 - 137
23GLUGLUMETMET(chain B and (resid 5 through 109 or resid 111 through 137 or resid 139 through 353))BB139 - 353139 - 353

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Components

#1: Protein Adenosine deaminase / / Adenosine aminohydrolase


Mass: 41812.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADA, ADA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00813, adenosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.49 M sodium phosphate monobasic monohydrate, 0.91 M potassium phosphate dibasic, pH 6.9

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.591→42.17 Å / Num. obs: 17712 / % possible obs: 75.67 % / Redundancy: 2.4 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.1201 / Rpim(I) all: 0.08772 / Rrim(I) all: 0.1495 / Χ2: 0.666 / Net I/σ(I): 7.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.591-2.6841.30.36971.754630.7570.9280.34060.50420.85224.7
2.63-2.681.50.333390.810.30.4480.83130.9
2.68-2.731.50.3554550.7580.3050.471.21641.6
2.73-2.791.70.3755390.70.3070.4870.96648.4
2.79-2.851.70.3696320.7640.3040.4810.8257.8
2.85-2.921.90.3487520.8060.2750.4460.98767.7
2.92-2.991.90.2928570.8580.2250.3710.88978.1
2.99-3.072.10.2869500.850.2210.3630.82886.3
3.07-3.162.30.26710210.8580.2030.3370.87291.9
3.16-3.262.40.2110470.9150.1580.2640.72493.9
3.26-3.382.40.1710250.9210.1280.2140.75793.1
3.38-3.512.70.14511020.9620.1030.1790.77698
3.51-3.672.80.11210800.9570.0790.1370.7298.1
3.67-3.872.70.08810920.9690.0630.1090.66698.5
3.87-4.112.80.06910970.9770.0480.0840.60997.7
4.11-4.432.70.05610650.9840.0390.0690.55995.4
4.43-4.872.50.04310520.9850.0310.0540.44994
4.87-5.582.70.04811070.9830.0340.0590.49697.5
5.58-7.022.80.0511140.9820.0350.0610.46498.4
7.02-502.60.03111190.9850.0220.0380.47694.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IAR

3iar


Resolution: 2.591→42.17 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 2405 9.94 %
Rwork0.2014 21793 -
obs0.2074 17712 56.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.5 Å2 / Biso mean: 42.3522 Å2 / Biso min: 14 Å2
Refinement stepCycle: final / Resolution: 2.591→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5550 0 2 24 5576
Biso mean--39.43 31.27 -
Num. residues----701
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2094X-RAY DIFFRACTION4.881TORSIONAL
12B2094X-RAY DIFFRACTION4.881TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.591-2.64350.5206240.392222510
2.6435-2.7010.3627340.360829613
2.701-2.76380.4589490.335142119
2.7638-2.83290.4109610.327452724
2.8329-2.90950.4071760.326464729
2.9095-2.99510.3392950.287485338
2.9951-3.09180.38091200.2944108347
3.0918-3.20220.32481360.2825121055
3.2022-3.33040.30291510.2651136060
3.3304-3.48190.30481680.2452153268
3.4819-3.66540.25181930.2019176177
3.6654-3.89490.2652140.1893189784
3.8949-4.19540.2442180.165196087
4.1954-4.61710.22932040.1533199087
4.6171-5.28420.20212150.1624193586
5.2842-6.65370.27132300.2105209993
6.6537-42.170.21472170.1837199787

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