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- PDB-1l8v: Crystal Structure of a Mutant (C109G,G212C) P4-P6 Domain of the G... -

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Basic information

Entry
Database: PDB / ID: 1l8v
TitleCrystal Structure of a Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron from Tetrahymena Thermophilia
ComponentsP4-P6 RNA ribozyme domain
KeywordsRNA / Ribozyme Domain / A-minor
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBattle, D.J. / Doudna, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Specificity of RNA-RNA Helix Recognition
Authors: Battle, D.J. / Doudna, J.A.
History
DepositionMar 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P4-P6 RNA ribozyme domain
B: P4-P6 RNA ribozyme domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,68712
Polymers101,4442
Non-polymers24310
Water4,252236
1
A: P4-P6 RNA ribozyme domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8446
Polymers50,7221
Non-polymers1225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P4-P6 RNA ribozyme domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8446
Polymers50,7221
Non-polymers1225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.455, 129.918, 144.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsthe biological assembly is a monomer

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Components

#1: RNA chain P4-P6 RNA ribozyme domain


Mass: 50722.113 Da / Num. of mol.: 2 / Mutation: C109G/G212C / Source method: obtained synthetically
Details: THE SEQUENCE IS A Synthetic construct from in-vitro transcription. It is based on the sequence from Tetrahymena Thermophilia.
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.73 Å3/Da / Density % sol: 67 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: MPD, magnesium chloride, cacodylate, spermine, sodium chloride, pH 6.5, VAPOR DIFFUSION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MgCl11
3cacodylate11
4spermine11
5NaCl11
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
122 %1reservoir
250 mMsodium cacodylate1reservoirpH6.5
30.05 mMspermine1reservoir
44 mg/mlprotein1drop
55 mMHEPES-NaOH1droppH7.5
65 mM1dropNaCl
740-70 mM1dropMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2001
RadiationMonochromator: Si(111) or (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. all: 38092 / Num. obs: 33255 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 63.2 Å2 / Net I/σ(I): 32.9
Reflection shellResolution: 2.8→2.98 Å / % possible all: 65.2
Reflection
*PLUS
Lowest resolution: 99 Å / Redundancy: 7 % / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 95.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GID

1gid


Resolution: 2.8→38.72 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 561769.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1670 5 %RANDOM
Rwork0.29 ---
all0.29 38092 --
obs0.29 33255 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 79.5611 Å2 / ksol: 0.318679 e/Å3
Displacement parametersBiso mean: 122.8 Å2
Baniso -1Baniso -2Baniso -3
1--42.06 Å20 Å20 Å2
2--84.76 Å20 Å2
3----42.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.56 Å
Luzzati d res low-5 Å
Luzzati sigma a0.91 Å1.17 Å
Refinement stepCycle: LAST / Resolution: 2.8→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6714 10 236 6960
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d15
X-RAY DIFFRACTIONc_improper_angle_d1.48
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.521 198 4.9 %
Rwork0.5497 3877 -
obs--65.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 99 Å / Rfactor all: 0.29 / Rfactor Rfree: 0.293 / Rfactor Rwork: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg15
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.48
LS refinement shell
*PLUS
Rfactor Rfree: 0.521 / Rfactor Rwork: 0.549

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