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- PDB-1r0v: Structure Determination of the Dimeric Endonuclease in a Pseudo-f... -

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Basic information

Entry
Database: PDB / ID: 1r0v
TitleStructure Determination of the Dimeric Endonuclease in a Pseudo-face-centerd P21212 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-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-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 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
C: tRNA-intron endonuclease
D: tRNA-intron endonuclease


Theoretical massNumber of molelcules
Total (without water)144,0014
Polymers144,0014
Non-polymers00
Water15,871881
1
A: tRNA-intron endonuclease
B: tRNA-intron endonuclease


Theoretical massNumber of molelcules
Total (without water)72,0002
Polymers72,0002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-9 kcal/mol
Surface area22730 Å2
MethodPISA
2
C: tRNA-intron endonuclease
D: tRNA-intron endonuclease


Theoretical massNumber of molelcules
Total (without water)72,0002
Polymers72,0002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-7 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.119, 144.149, 52.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-515-

HOH

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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.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / 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: 1.9 Å3/Da / Density % sol: 34.9 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→500 Å / Num. all: 61664 / Num. obs: 60298 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.5 Å2
Reflection shellHighest resolution: 2 Å / % possible all: 90.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→95.35 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3220 5.1 %RANDOM
Rwork0.1736 ---
all0.1771 61664 --
obs0.1771 60298 92.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1658 Å2 / ksol: 0.374143 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-13.4 Å20 Å20 Å2
2---6.78 Å20 Å2
3----6.62 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å / Luzzati sigma a free: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8192 0 0 881 9073
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.043
X-RAY DIFFRACTIONc_angle_deg3.288
X-RAY DIFFRACTIONc_dihedral_angle_d8.623
X-RAY DIFFRACTIONc_improper_angle_d0.271
LS refinement shellHighest resolution: 2 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork7797 -
Rfree-4.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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