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- PDB-2nx8: The crystal structure of the tRNA-specific adenosine deaminase fr... -

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Basic information

Entry
Database: PDB / ID: 2nx8
TitleThe crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes
ComponentsTRNA-specific adenosine deaminase
KeywordsHYDROLASE / tRNA / adenosine / deaminase / tad
Function / homology
Function and homology information


tRNA(adenine34) deaminase / tRNA wobble adenosine to inosine editing / tRNA-specific adenosine-34 deaminase activity / zinc ion binding
Similarity search - Function
MafB19-like deaminase / tRNA-specific adenosine deaminase / 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
PHOSPHATE ION / tRNA-specific adenosine deaminase
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsHwang, K.Y. / Lee, W.-H. / Kim, Y.K.
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes
Authors: Lee, W.-H. / Kim, Y.K. / Nam, K.H. / Priyadarshi, A. / Lee, E.H. / Kim, E.E. / Jeon, Y.H. / Cheong, C. / Hwang, K.Y.
History
DepositionNov 17, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The first 8 residues(MELGESFL) are not present in UniProt entry(Q5XE14 Y214_STRP6), though ...SEQUENCE The first 8 residues(MELGESFL) are not present in UniProt entry(Q5XE14 Y214_STRP6), though are present in the original translation from the underlying genomic DNA sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRNA-specific adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3983
Polymers20,2371
Non-polymers1602
Water2,486138
1
A: TRNA-specific adenosine deaminase
hetero molecules

A: TRNA-specific adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7956
Polymers40,4742
Non-polymers3214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3480 Å2
ΔGint-115 kcal/mol
Surface area16330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.091, 80.091, 81.104
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 TRNA-specific adenosine deaminase / Hypothetical protein M6_Spy0214


Mass: 20237.133 Da / Num. of mol.: 1 / Mutation: A27S/A122V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M6 (bacteria)
Species: Streptococcus pyogenes / Strain: MGAS10394 / Plasmid: pET 22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 DE3
References: UniProt: Q5XE14, 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.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 5

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.7 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 2% PEG 1000, 1.7M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2834, 1.2827, 1.2573, 1.28
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2004
RadiationMonochromator: Wiggler / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28341
21.28271
31.25731
41.281
ReflectionResolution: 2→20 Å / Num. obs: 30630 / % possible obs: 89.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.078 / Net I/σ(I): 29.6
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.081 / % possible all: 89.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.66 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 349075.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1482 4.8 %RANDOM
Rwork0.214 ---
obs0.214 30630 89.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.1025 Å2 / ksol: 0.403394 e/Å3
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å20 Å20 Å2
2--2.78 Å20 Å2
3----5.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 6 138 1470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 181 4.7 %
Rwork0.3 3689 -
obs--68.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5po4.parpo4.top

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