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- PDB-3dh1: Crystal structure of human tRNA-specific adenosine-34 deaminase s... -

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Basic information

Entry
Database: PDB / ID: 3dh1
TitleCrystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2
ComponentstRNA-specific adenosine deaminase 2
KeywordsHYDROLASE / tRNA-specific adenosine deaminase / zinc-binding protein / translation / tRNA processing / structural genomics / Structural Genomics Consortium / SGC / Metal-binding
Function / homology
Function and homology information


tRNA-specific adenosine-34 deaminase complex / tRNA(adenine34) deaminase / tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / tRNA modification in the nucleus and cytosol / tRNA modification / zinc ion binding / nucleoplasm
Similarity search - Function
tRNA-specific adenosine deaminase / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA-specific adenosine deaminase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWelin, M. / Tresaugues, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. ...Welin, M. / Tresaugues, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / van der Berg, S. / Wisniewska, M. / Wikstrom, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human tRNA-specific adenosine-34 deaminase subunit ADAT2.
Authors: Welin, M. / Tresaugues, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...Authors: Welin, M. / Tresaugues, L. / Andersson, J. / Arrowsmith, C.H. / Berglund, H. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Lehtio, L. / Moche, M. / Nilsson, M.E. / Nyman, T. / Olesen, K. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / van der Berg, S. / Wisniewska, M. / Wikstrom, M. / Nordlund, P.
History
DepositionJun 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_ncs_dom_lim / 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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: tRNA-specific adenosine deaminase 2
B: tRNA-specific adenosine deaminase 2
C: tRNA-specific adenosine deaminase 2
D: tRNA-specific adenosine deaminase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5638
Polymers85,3014
Non-polymers2624
Water724
1
A: tRNA-specific adenosine deaminase 2
D: tRNA-specific adenosine deaminase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7824
Polymers42,6512
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-25.4 kcal/mol
Surface area15480 Å2
MethodPISA
2
B: tRNA-specific adenosine deaminase 2
C: tRNA-specific adenosine deaminase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7824
Polymers42,6512
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-24.3 kcal/mol
Surface area15020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.530, 103.120, 77.590
Angle α, β, γ (deg.)90.00, 97.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 13 - 172 / Label seq-ID: 17 - 176

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
tRNA-specific adenosine deaminase 2 / tRNA-specific adenosine-34 deaminase subunit ADAT2 / Deaminase domain-containing protein 1


Mass: 21325.348 Da / Num. of mol.: 4 / Fragment: Residues 20-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAT2, DEADC1 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE
References: UniProt: Q7Z6V5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M Ammonium acetate, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2813 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2008 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2813 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 18343 / Num. obs: 18284 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 25.535 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 12.64
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.84 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 3.88 / Num. unique all: 1802 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NX8

2nx8


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.884 / SU B: 33.561 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25614 912 5 %RANDOM
Rwork0.20237 ---
obs0.20502 17318 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.535 Å2
Baniso -1Baniso -2Baniso -3
1--2.81 Å20 Å2-1.36 Å2
2--5.42 Å20 Å2
3----2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5043 0 4 4 5051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225139
X-RAY DIFFRACTIONr_bond_other_d0.0180.023458
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.9556948
X-RAY DIFFRACTIONr_angle_other_deg1.06238461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95325.062243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74115910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.051528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025729
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02983
X-RAY DIFFRACTIONr_nbd_refined0.220.21137
X-RAY DIFFRACTIONr_nbd_other0.1810.23423
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22444
X-RAY DIFFRACTIONr_nbtor_other0.090.22701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.270
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.222
X-RAY DIFFRACTIONr_mcbond_it0.6751.54123
X-RAY DIFFRACTIONr_mcbond_other0.111.51294
X-RAY DIFFRACTIONr_mcangle_it0.66525160
X-RAY DIFFRACTIONr_scbond_it1.21932258
X-RAY DIFFRACTIONr_scangle_it1.6844.51788
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A942medium positional0.110.5
2B942medium positional0.120
3C942medium positional0.120
4D942medium positional0.120
1A1172loose positional0.35
2B1172loose positional0.30
3C1172loose positional0.30
4D1172loose positional0.30
1A942medium thermal0.422
2B942medium thermal0.340
3C942medium thermal0.390
4D942medium thermal0.390
1A1172loose thermal0.610
2B1172loose thermal0.520.01
3C1172loose thermal0.510
4D1172loose thermal0.50
LS refinement shellResolution: 2.8→2.871 Å / Rfactor Rfree error: 0.394 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 66 -
Rwork0.274 1243 -
obs-1243 100 %
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)
12.14344.0518-1.333318.9055-9.626215.50920.2061-0.61480.27490.30060.19250.4201-0.76980.2017-0.3985-0.05080.00320.0506-0.0259-0.163-0.13339.983421.926550.3529
23.6879-1.4893.73972.2023-3.730311.3789-0.13220.36350.6111-0.0423-0.1807-0.4686-1.24720.46560.31290.1961-0.0049-0.00490.0510.01540.233915.066225.490534.7695
32.4881-0.30080.55761.77830.92044.33940.09180.12890.0712-0.14820.0288-0.05770.15870.099-0.12070.02120.00760.03820.01660.02560.082413.305712.711733.7554
42.69811.7648-0.63969.9464-5.896810.006-0.00330.12940.7119-0.2209-0.0541-0.0336-0.7268-0.37310.05750.07810.064-0.02460.1346-0.00050.22644.086622.903329.368
58.8869-7.4891-7.272341.674721.027918.64740.30080.59480.7944-0.2278-0.0014-0.5795-0.4819-0.541-0.2994-0.16170.0786-0.0564-0.04830.1131-0.0976-5.490317.47239.9784
62.413-2.2223-2.2633.48115.713919.03-0.06030.01660.31890.3999-0.0640.3637-0.3746-1.69180.12420.07070.03110.0010.31640.02780.2253-11.689818.061455.0925
71.8441-0.09520.52993.39290.43075.4948-0.0559-0.1614-0.00380.15880.06670.19870.2803-0.3087-0.01090.02950.01730.03650.17250.00540.0567-3.4678.415456.5863
87.9442-1.6535-2.94064.85533.360810.08960.0724-0.27370.92010.2541-0.08030.4242-0.784-0.1240.00780.0750.0055-0.01460.1730.00520.1698-1.464922.144559.3293
916.3244-10.6973-10.885721.233213.208615.7057-0.1923-1.3183-0.58660.48590.4476-0.27511.613-0.022-0.25530.3304-0.0246-0.02790.00230.1242-0.1894-1.7156-10.956687.8829
1028.985530.8893-26.038236.1149-24.261527.1938-0.10720.3704-0.07061.3353-0.2608-0.91240.3819-0.15160.36790.58280.0606-0.11640.30870.04010.0424-0.6842-16.503479.1583
112.80210.31-0.52520.857-0.72146.7940.0142-0.0061-0.4468-0.14860.02290.30290.7346-0.729-0.03710.2815-0.0503-0.02180.25480.01940.1834-4.5552-6.206871.0695
125.4638-1.36580.40337.1020.63665.05450.0660.237-0.1373-0.04350.1113-0.48510.64530.4231-0.17720.19880.02140.00870.2542-0.00870.08679.0275-4.581569.8712
135.4432-8.34078.912440.1583-23.095119.50250.27740.7056-0.4787-0.3491-0.3323-0.59621.05830.82330.0550.05490.13870.0260.1551-0.1741-0.121325.4743-5.92624.9329
143.08220.19-1.3491.9845-7.118425.67920.0178-0.1224-0.38920.0837-0.1631-0.63910.85011.20.14530.30570.1211-0.01830.2058-0.05890.197427.4944-6.400821.1653
151.83910.3635-0.79332.3263-0.21135.5596-0.00160.14610.0778-0.01570.0653-0.14910.1190.2738-0.06360.12110.0413-0.01340.14070.02060.088618.49682.814419.7924
1611.74984.18661.85458.73086.899443.54840.4388-0.3465-0.88840.26190.0229-0.33362.3522-0.1917-0.46160.5440.0767-0.1379-0.00580.04580.540718.888-15.091128.3774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 2416 - 28
2X-RAY DIFFRACTION2AA25 - 5929 - 63
3X-RAY DIFFRACTION3AA60 - 14964 - 153
4X-RAY DIFFRACTION4AA150 - 173154 - 177
5X-RAY DIFFRACTION5BB13 - 2417 - 28
6X-RAY DIFFRACTION6BB25 - 5329 - 57
7X-RAY DIFFRACTION7BB54 - 14958 - 153
8X-RAY DIFFRACTION8BB150 - 172154 - 176
9X-RAY DIFFRACTION9CC13 - 2317 - 27
10X-RAY DIFFRACTION10CC24 - 2728 - 31
11X-RAY DIFFRACTION11CC28 - 12532 - 129
12X-RAY DIFFRACTION12CC126 - 172130 - 176
13X-RAY DIFFRACTION13DD13 - 2417 - 28
14X-RAY DIFFRACTION14DD25 - 5329 - 57
15X-RAY DIFFRACTION15DD54 - 15758 - 161
16X-RAY DIFFRACTION16DD158 - 173162 - 177

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