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- PDB-6d8l: Group I self-splicing intron P4-P6 domain mutant U131A (without i... -

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Basic information

Entry
Database: PDB / ID: 6d8l
TitleGroup I self-splicing intron P4-P6 domain mutant U131A (without isopropanol soaking)
ComponentsGroup I self-splicing intron
KeywordsRNA / ribozyme
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.14021549796 Å
AuthorsShoffner, G.M.
CitationJournal: Structure / Year: 2018
Title: In Crystallo Selection to Establish New RNA Crystal Contacts.
Authors: Shoffner, G.M. / Wang, R. / Podell, E. / Cech, T.R. / Guo, F.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Group I self-splicing intron
B: Group I self-splicing intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,68324
Polymers102,1492
Non-polymers53522
Water543
1
A: Group I self-splicing intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,36613
Polymers51,0741
Non-polymers29212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Group I self-splicing intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,31711
Polymers51,0741
Non-polymers24310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.480, 132.950, 147.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: RNA chain Group I self-splicing intron


Mass: 51074.363 Da / Num. of mol.: 2 / Fragment: P4-P6 domain / Mutation: U131A / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote) / References: GenBank: 10832
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.62 Å3/Da / Density % sol: 66.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: MPD, sodium cacodylate, cobalt hexamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.14→67.2 Å / Num. obs: 25498 / % possible obs: 95.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 108.199921507 Å2 / Net I/σ(I): 12.9
Reflection shellResolution: 3.14→3.22 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GID

1gid


Resolution: 3.14021549796→67.1969620749 Å / SU ML: 0.388983508324 / Cross valid method: FREE R-VALUE / σ(F): 1.35526318651 / Phase error: 32.720501367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.269597607208 2551 10.0047062515 %
Rwork0.250350329162 22947 -
obs0.251022611814 25498 95.813918533 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.143898322 Å2
Refinement stepCycle: LAST / Resolution: 3.14021549796→67.1969620749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6770 22 3 6795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002971421797457580
X-RAY DIFFRACTIONf_angle_d0.73163390376111818
X-RAY DIFFRACTIONf_chiral_restr0.04279082228471580
X-RAY DIFFRACTIONf_plane_restr0.00423060178505316
X-RAY DIFFRACTIONf_dihedral_angle_d14.56635011443786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1402-3.20060.4639192048031160.4667086950071038X-RAY DIFFRACTION80.3061934586
3.2006-3.26590.3929686414921320.394678091451196X-RAY DIFFRACTION90.8344733242
3.2659-3.3370.351849877851320.3947659840261186X-RAY DIFFRACTION92.3615977575
3.337-3.41460.4072248473761370.3579393138381236X-RAY DIFFRACTION93.0216802168
3.4146-3.50.3555946774561350.3336296411461203X-RAY DIFFRACTION91.4559125085
3.5-3.59460.2783443433151390.3180038765121250X-RAY DIFFRACTION95.1369863014
3.5946-3.70040.3208211102771370.2804657160381235X-RAY DIFFRACTION95.8770090846
3.7004-3.81980.3209227416361410.2702712213621262X-RAY DIFFRACTION95.5071477195
3.8198-3.95630.311497045021420.2506264569891292X-RAY DIFFRACTION96.8264686023
3.9563-4.11470.2329222210421420.2396754569591282X-RAY DIFFRACTION98.1392143349
4.1147-4.30190.2132055449641450.2340610706531299X-RAY DIFFRACTION97.8319783198
4.3019-4.52870.1993391994221440.2239878396141302X-RAY DIFFRACTION98.8380041012
4.5287-4.81230.2656892689341470.2201579281411322X-RAY DIFFRACTION98.9225589226
4.8123-5.18380.2367979304251480.2040336862351331X-RAY DIFFRACTION99.7302764666
5.1838-5.70520.2451614375321500.2082225545891349X-RAY DIFFRACTION99.8002663116
5.7052-6.53010.2413532904521490.2106250395621341X-RAY DIFFRACTION99.8659517426
6.5301-8.22490.2434320723391540.2217850165771381X-RAY DIFFRACTION99.8049414824
8.2249-67.21230.2818075664251610.264836160561442X-RAY DIFFRACTION99.3184634449

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