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- PDB-1ryb: Crystal Structure of the Chloroplast Group II Intron Splicing Fac... -

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Basic information

Entry
Database: PDB / ID: 1ryb
TitleCrystal Structure of the Chloroplast Group II Intron Splicing Factor CRS2
ComponentsCRS2
KeywordsHYDROLASE / ALPHA-BETA
Function / homology
Function and homology information


aminoacyl-tRNA hydrolase activity / chloroplast stroma / RNA splicing / mRNA processing / ribonucleoprotein complex
Similarity search - Function
: / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase signature 1. / Peptidyl-tRNA hydrolase / Peptidyl-tRNA hydrolase, conserved site / Peptidyl-tRNA hydrolase superfamily / Peptidyl-tRNA hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chloroplastic group IIB intron splicing facilitator CRS2, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOstheimer, G.J. / Barkan, A. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces
Authors: Ostheimer, G.J. / Hadjivasiliou, H. / Kloer, D.P. / Barkan, A. / Matthews, B.W.
History
DepositionDec 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: CRS2


Theoretical massNumber of molelcules
Total (without water)22,6771
Polymers22,6771
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.375, 62.644, 78.235
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRS2


Mass: 22676.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: crs2 / Plasmid: pQE40 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9M5P4, peptidyl-tRNA hydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.89 Å3/Da / Density % sol: 34.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: PEG 4000, CAPS, sodium chloride, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
224 %PEG34001reservoir
3100 mM1reservoirNaCl
4100 mMCAPS1reservoirpH10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.773 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.773 Å / Relative weight: 1
ReflectionResolution: 1.7→13 Å / Num. all: 20295 / Num. obs: 20208 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 15.5 Å2 / Rsym value: 0.052 / Net I/σ(I): 8.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 10361 / Rsym value: 0.194 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 13.1 Å / Num. obs: 20160 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.194

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
TNTrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PTH

2pth


Resolution: 1.7→12 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1031 -RANDOM
Rwork0.173 ---
obs0.176 20208 99.6 %-
all-20295 --
Refinement stepCycle: LAST / Resolution: 1.7→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1446 0 0 164 1610
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.021
X-RAY DIFFRACTIONt_dihedral_angle_d2.8
Refinement
*PLUS
Lowest resolution: 13.1 Å / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg2.8

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