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- PDB-3rys: The crystal structure of adenine deaminase (AAur1117) from Arthro... -

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Basic information

Entry
Database: PDB / ID: 3rys
TitleThe crystal structure of adenine deaminase (AAur1117) from Arthrobacter aurescens
ComponentsAdenosine deaminase 1
KeywordsHYDROLASE / SGX
Function / homology
Function and homology information


adenine deaminase / adenine deaminase activity / adenine catabolic process / hypoxanthine salvage / nucleotide metabolic process / zinc ion binding
Similarity search - Function
Adenine deaminase type 2 / 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
ADENINE / Adenine deaminase
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsZhang, Z. / Goble, A.M. / Raushel, F.M. / Swaminathan, S.
CitationJournal: To be Published
Title: The crystal structure of adenine deaminase (AAur1117) from Arthrobacter aurescens
Authors: Zhang, Z. / Goble, A.M. / Raushel, F.M. / Swaminathan, S.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / 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_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_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 1
B: Adenosine deaminase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6506
Polymers75,2482
Non-polymers4014
Water1,38777
1
A: Adenosine deaminase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8253
Polymers37,6241
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine deaminase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8253
Polymers37,6241
Non-polymers2012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.104, 124.104, 89.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Adenosine deaminase 1 / / adenine deaminase / AAur1117 / adenosine aminohydrolase 1


Mass: 37624.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: add, add1, AAur_1117 / Plasmid: pET-30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A1R3U3, 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-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride hexahydrate, 30% w/v PEG4000, 10 mM adenine, 0.1 M Tris hydrochloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22144 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Rmerge(I) obs: 0.149 / Net I/σ(I): 19.83
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 8.7 / Num. unique all: 2167 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OU8

3ou8


Resolution: 2.601→47.201 Å / SU ML: 0.34 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.3 / Phase error: 23.81 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1089 5.1 %RANDOM
Rwork0.2 ---
obs0.2029 21346 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.299 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 21.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.1836 Å20 Å20 Å2
2--0.1836 Å2-0 Å2
3----0.3672 Å2
Refinement stepCycle: LAST / Resolution: 2.601→47.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5100 0 22 77 5199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045207
X-RAY DIFFRACTIONf_angle_d0.7677082
X-RAY DIFFRACTIONf_dihedral_angle_d16.6591880
X-RAY DIFFRACTIONf_chiral_restr0.052817
X-RAY DIFFRACTIONf_plane_restr0.003941
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6005-2.71890.32811400.24342360X-RAY DIFFRACTION92
2.7189-2.86220.30861230.23812419X-RAY DIFFRACTION94
2.8622-3.04150.32141220.23112470X-RAY DIFFRACTION95
3.0415-3.27630.27741410.21672500X-RAY DIFFRACTION96
3.2763-3.60590.27111390.20122532X-RAY DIFFRACTION98
3.6059-4.12740.22291500.16492586X-RAY DIFFRACTION99
4.1274-5.1990.18251380.15782617X-RAY DIFFRACTION99
5.199-47.20830.22321360.18992773X-RAY DIFFRACTION99

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