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- PDB-1r11: Structure Determination of the Dimeric Endonuclease in a Pseudo-f... -

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Basic information

Entry
Database: PDB / ID: 1r11
TitleStructure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21 space group
ComponentstRNA-intron endonuclease
KeywordsTRANSLATION / HYDROLASE / RNA splicing / endonuclease / x-ray crystallography
Function / homology
Function and homology information


tRNA-intron lyase / tRNA-intron endonuclease activity / tRNA splicing, via endonucleolytic cleavage and ligation / nucleic acid binding / lyase activity
Similarity search - Function
Trna Endonuclease; Chain: A, domain 1 - #150 / tRNA-splicing endonuclease, archaeal long subfamily / tRNA intron endonuclease, N-terminal domain / tRNA intron endonuclease, N-terminal domain superfamily / tRNA intron endonuclease, N-terminal / tRNA intron endonuclease, N-terminal domain / tRNA-splicing endonuclease / 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 - #150 / tRNA-splicing endonuclease, archaeal long subfamily / tRNA intron endonuclease, N-terminal domain / tRNA intron endonuclease, N-terminal domain superfamily / tRNA intron endonuclease, N-terminal / tRNA intron endonuclease, N-terminal domain / tRNA-splicing endonuclease / 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 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / MutS, DNA mismatch repair protein, domain I / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA-splicing endonuclease
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, H. / Zhang, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure determination of a truncated dimeric splicing endonuclease in pseudo-face-centered space group P2(1)2(1)2.
Authors: Zhang, Y. / Li, H.
History
DepositionSep 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-intron endonuclease
B: tRNA-intron endonuclease


Theoretical massNumber of molelcules
Total (without water)72,0002
Polymers72,0002
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-10 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.412, 74.169, 84.855
Angle α, β, γ (deg.)90.00, 106.13, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein tRNA-intron endonuclease / / E.C.3.1.27.9 / Splicing Endonuclease / intron endonuclease / endA


Mass: 36000.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: ENDA / Production host: Escherichia coli (E. coli) / References: UniProt: O29362, EC: 3.1.27.9

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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: 2.24 Å3/Da / Density % sol: 44.8 %
Crystal growpH: 6.6
Details: 100 mM Na-cacodylic acid pH 6.5 - 6.8, 20 mM (NH4)2SO4, 300-400 mM NaCH2COOH, pH 6.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 6.8 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoirpH6.5-6.8
320 mMammonium sulfate1reservoir
4300-400 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→500 Å / Num. all: 17717 / Num. obs: 17292 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 22 Å2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 77465 / % possible obs: 90.8 % / Redundancy: 3.89 % / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 76.5 % / Redundancy: 2.46 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→26.66 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2927 1410 4.7 %RANDOM
Rwork0.2306 ---
all0.249 13334 --
obs0.2369 12664 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.1469 Å2 / ksol: 0.382405 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å25.88 Å2
2--3.22 Å20 Å2
3----1.65 Å2
Refine analyzeLuzzati coordinate error free: 0.4 Å / Luzzati sigma a free: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→26.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 0 0 5042
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.032
X-RAY DIFFRACTIONc_angle_deg2.766
X-RAY DIFFRACTIONc_dihedral_angle_d8.339
X-RAY DIFFRACTIONc_improper_angle_d3.38
LS refinement shellHighest resolution: 2.7 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork1645 -
Rfree-2.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.1856
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.163
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg8.339
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.38
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / Rfactor Rfree: 0.307 / Rfactor Rwork: 0.233

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