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- PDB-3ocq: crystal structure of tRNA-specific Adenosine deaminase from Salmo... -

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Basic information

Entry
Database: PDB / ID: 3ocq
Titlecrystal structure of tRNA-specific Adenosine deaminase from Salmonella enterica
ComponentsPutative Cytosine/adenosine deaminase
KeywordsHYDROLASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / Nucleoside deaminases / Zn binding
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
tRNA-specific adenosine deaminase / MafB19-like 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
tRNA-specific adenosine deaminase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKim, J. / Ramagopal, U.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of tRNA-specific Adenosine deaminase from Salmonella enterica
Authors: Kim, J. / Ramagopal, U.A. / Burley, S.K. / Almo, S.C.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative Cytosine/adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3862
Polymers20,3201
Non-polymers651
Water66737
1
A: Putative Cytosine/adenosine deaminase
hetero molecules

A: Putative Cytosine/adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7724
Polymers40,6412
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area2840 Å2
ΔGint-103 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.490, 75.490, 44.757
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Putative Cytosine/adenosine deaminase


Mass: 20320.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: SCH_2563, yfhC / Plasmid: LIC-PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q57LE3, adenosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 1.81 Å3/Da / Density % sol: 32.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES ph 6.5, 12% PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2009
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 9510 / Num. obs: 9067 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 41.99 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.062 / Net I/σ(I): 14.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 2.3 / Num. unique all: 731 / Rsym value: 0.307 / % possible all: 81.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z3A

1z3a


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.811 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.238 435 4.8 %RANDOM
Rwork0.18606 ---
obs0.18862 8634 95.64 %-
all-9482 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.425 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å2-0.85 Å20 Å2
2---1.7 Å20 Å2
3---2.55 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1141 0 1 37 1179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211167
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9351583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0721.66754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90915190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.8971513
X-RAY DIFFRACTIONr_chiral_restr0.1130.2177
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021888
X-RAY DIFFRACTIONr_mcbond_it1.1471.5721
X-RAY DIFFRACTIONr_mcangle_it1.91821153
X-RAY DIFFRACTIONr_scbond_it3.3613446
X-RAY DIFFRACTIONr_scangle_it5.3344.5430
LS refinement shellResolution: 2.052→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 21 -
Rwork0.22 557 -
obs-557 84.38 %
Refinement TLS params.Method: refined / Origin x: 1.441 Å / Origin y: 25.628 Å / Origin z: 18.736 Å
111213212223313233
T0.06 Å20.0217 Å2-0.065 Å2-0.0388 Å2-0.021 Å2--0.1402 Å2
L1.7885 °2-0.8901 °20.2943 °2-0.9632 °2-0.2082 °2--0.4496 °2
S0.0231 Å °0.0364 Å °-0.0375 Å °-0.0484 Å °-0.1504 Å °0.1819 Å °-0.0756 Å °0.0363 Å °0.1273 Å °

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