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- PDB-3iar: The crystal structure of human adenosine deaminase -

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Basic information

Entry
Database: PDB / ID: 3iar
TitleThe crystal structure of human adenosine deaminase
ComponentsAdenosine deaminase
KeywordsHYDROLASE / deaminase / adenosine deaminase / adenosine / purine metabolism / Structural Genomics / Structural Genomics Consortium / SGC / Disease mutation / Hereditary hemolytic anemia / Nucleotide metabolism / SCID
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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-3D1 / NICKEL (II) ION / NITRATE ION / Adenosine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsUgochukwu, E. / Zhang, Y. / Hapka, E. / Yue, W.W. / Bray, J.E. / Muniz, J. / Burgess-Brown, N. / Chaikuad, A. / von Delft, F. / Bountra, C. ...Ugochukwu, E. / Zhang, Y. / Hapka, E. / Yue, W.W. / Bray, J.E. / Muniz, J. / Burgess-Brown, N. / Chaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of human adenosine deaminase
Authors: Ugochukwu, E. / Zhang, Y. / Hapka, E. / Yue, W.W. / Bray, J.E. / Muniz, J. / Burgess-Brown, N. / Chaikuad, A. / Kavanagh, K.L. / Oppermann, U.
History
DepositionJul 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9086
Polymers41,3821
Non-polymers5265
Water12,448691
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.070, 73.510, 76.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Adenosine deaminase / / Adenosine aminohydrolase


Mass: 41381.988 Da / Num. of mol.: 1 / Fragment: UNP residues 5-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADA / Plasmid: pNIC-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: P00813, adenosine deaminase

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Non-polymers , 5 types, 696 molecules

#2: Chemical ChemComp-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O3
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.20M NaNO3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.52→29.698 Å / Num. obs: 52538 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 18.6
Reflection shellResolution: 1.52→1.6 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 3.1 / Num. unique all: 14424 / Rsym value: 0.251 / % possible all: 86.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KRM

1krm


Resolution: 1.52→29.698 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1849 1901 3.63 %RANDOM
Rwork0.1526 ---
obs0.1537 52324 97.29 %-
all-0 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.941 Å2 / ksol: 0.318 e/Å3
Refinement stepCycle: LAST / Resolution: 1.52→29.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 33 691 3559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143020
X-RAY DIFFRACTIONf_angle_d1.5184106
X-RAY DIFFRACTIONf_dihedral_angle_d16.2241123
X-RAY DIFFRACTIONf_chiral_restr0.098444
X-RAY DIFFRACTIONf_plane_restr0.009540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.5580.21911050.19392765X-RAY DIFFRACTION76
1.558-1.60020.20531340.1683342X-RAY DIFFRACTION92
1.6002-1.64720.16731290.14953585X-RAY DIFFRACTION98
1.6472-1.70040.16451510.13733645X-RAY DIFFRACTION99
1.7004-1.76120.17261310.1343628X-RAY DIFFRACTION100
1.7612-1.83170.15751340.13593675X-RAY DIFFRACTION100
1.8317-1.9150.20471330.13343675X-RAY DIFFRACTION100
1.915-2.0160.17961460.12993655X-RAY DIFFRACTION100
2.016-2.14220.17431370.1283678X-RAY DIFFRACTION100
2.1422-2.30760.15981420.1243706X-RAY DIFFRACTION100
2.3076-2.53970.1661400.13413704X-RAY DIFFRACTION100
2.5397-2.90690.1641350.1363740X-RAY DIFFRACTION100
2.9069-3.66130.15131410.12893756X-RAY DIFFRACTION100
3.6613-29.70350.17071430.1363869X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1280.03340.19020.0410.00080.0419-0.01960.0749-0.0133-0.04110.0249-0.0058-0.02980.0284-0.00480.0861-0.00440.00360.082-0.0116-0.00949.27137.4552-4.6709
20.0787-0.03220.01690.1254-0.0810.01110.01490.0012-0.00460.0749-0.0198-0.0149-0.04080.00240.00810.07920.0009-0.01480.0609-0.0007-0.0258.77352.29689.4301
31.0419-0.01770.733-0.18870.04411.69560.0299-0.0331-0.12690.02750.02890.0074-0.0428-0.0962-0.06260.0703-0.0065-0.00350.03680.00790.007-1.0428-12.36619.2914
40.72380.0304-0.3652-0.20190.08770.81450.01320.0044-0.1347-0.0091-0.0072-0.0676-0.07060.008-0.00380.0857-0.02730.01390.0875-0.01550.0791-12.4473-15.79573.1508
50.244-0.0116-0.05910.1657-0.072-0.22510.01720.0314-0.012-0.0243-0.01120.0108-0.03670.014-0.00170.05610.0013-0.00660.0629-0.0156-0.0274-10.2726-0.4035-2.7503
6-0.00070.02830.03640.18220.0450.13820.0087-0.00940.00720.12160.0230.0384-0.0673-0.1546-0.03030.06140.00490.02920.08510.00020.0049-21.49767.956512.5073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:74)A3 - 74
2X-RAY DIFFRACTION2(chain A and resid 75:196)A75 - 196
3X-RAY DIFFRACTION3(chain A and resid 197:238)A197 - 238
4X-RAY DIFFRACTION4(chain A and resid 239:256)A239 - 256
5X-RAY DIFFRACTION5(chain A and resid 257:339)A257 - 339
6X-RAY DIFFRACTION6(chain A and resid 340:362)A340 - 362

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