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- PDB-3if0: Crystal Structure of the Nanoarchaeum equitans tRNA splicing endo... -

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Basic information

Entry
Database: PDB / ID: 3if0
TitleCrystal Structure of the Nanoarchaeum equitans tRNA splicing endonuclease structural subunit
ComponentsNEQ261
KeywordsHYDROLASE / protein
Function / homology
Function and homology information


tRNA-intron lyase activity / tRNA splicing, via endonucleolytic cleavage and ligation
Similarity search - Function
tRNA-splicing endonuclease subunit NEQ261 N-terminal domain / Trna Endonuclease; Chain: A, domain 1 - #150 / tRNA intron endonuclease, catalytic domain-like / tRNA intron endonuclease, catalytic C-terminal domain / tRNA intron endonuclease, catalytic domain-like superfamily / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNanoarchaeum equitans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsMitchell, M. / Li, H.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Crystal structure and assembly of the functional Nanoarchaeum equitans tRNA splicing endonuclease.
Authors: Mitchell, M. / Xue, S. / Erdman, R. / Randau, L. / Soll, D. / Li, H.
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
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
X: NEQ261


Theoretical massNumber of molelcules
Total (without water)18,4491
Polymers18,4491
Non-polymers00
Water00
1
X: NEQ261

X: NEQ261


Theoretical massNumber of molelcules
Total (without water)36,8972
Polymers36,8972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area2420 Å2
ΔGint-19 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.434, 95.434, 47.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NEQ261


Mass: 18448.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nanoarchaeum equitans (archaea) / Gene: NEQ261 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q74MS9

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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: 3.41 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.10 M sodium acetate pH 4.6, 0.30 M ammonium acetate, 35% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2009
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 13062 / Num. obs: 13062 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 8 / Redundancy: 19 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.624 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IEY

3iey


Resolution: 2.2→41.38 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.168 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27712 643 5 %RANDOM
Rwork0.24827 ---
obs0.24964 12345 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å20 Å2
2--0.39 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 0 0 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9821752
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09323.22662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38815251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.382159
X-RAY DIFFRACTIONr_chiral_restr0.1030.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021968
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6461.5740
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20621203
X-RAY DIFFRACTIONr_scbond_it1.7473561
X-RAY DIFFRACTIONr_scangle_it2.8534.5549
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 50 -
Rwork0.277 907 -
obs--99.9 %
Refinement TLS params.Method: refined / Origin x: 27.6367 Å / Origin y: -21.9329 Å / Origin z: 6.3322 Å
111213212223313233
T0.0885 Å2-0.0305 Å2-0.0306 Å2-0.0878 Å20.0143 Å2--0.048 Å2
L2.2978 °20.2771 °21.1937 °2-1.2946 °20.606 °2--1.3721 °2
S-0.0712 Å °-0.0781 Å °0.2102 Å °0.0363 Å °-0.0753 Å °-0.0626 Å °-0.0489 Å °-0.021 Å °0.1465 Å °

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