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- PDB-1hr2: CRYSTAL STRUCTURE ANALYSIS OF A MUTANT P4-P6 DOMAIN (DELC209) OF ... -

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Entry
Database: PDB / ID: 1hr2
TitleCRYSTAL STRUCTURE ANALYSIS OF A MUTANT P4-P6 DOMAIN (DELC209) OF TETRAHYMENA THEMOPHILA GROUP I INTRON.
ComponentsP4-P6 DELC209 MUTANT RNA RIBOZYME DOMAIN
KeywordsRNA / P4-P6 / C209 / RIBOZYME / TETRAHYMENA / GROUP I INTRON / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsJuneau, K. / Podell, E.R. / Harrington, D.J. / Cech, T.R.
Citation
Journal: Structure / Year: 2001
Title: Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions.
Authors: Juneau, K. / Podell, E. / Harrington, D.J. / Cech, T.R.
#1: Journal: RNA / Year: 1999
Title: In-Vitro Selection of RNAs With Increased Tertiary Structure Stability
Authors: Juneau, K. / Cech, T.R.
#2: Journal: Science / Year: 1996
Title: Crystal Structure of a Group I Ribozyme Domain: Principles of RNA Packing
Authors: Cate, J.H. / Gooding, A.R. / Podell, E. / Zhou, K. / Golden, B.L. / Kundrot, C.E. / Cech, T.R. / A Doudna, J.
#3: Journal: Structure / Year: 1996
Title: Metal-binding Sites in the Major Groove of a Large Ribozyme Domain
Authors: Cate, J.H. / Doudna, J.A.
#4: Journal: Nat.Struct.Biol. / Year: 1997
Title: A Magnesium Ion Core at the Heart of a Ribozyme Domain
Authors: Cate, J.H. / Hanna, R.L. / Doudna, J.A.
History
DepositionDec 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_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 DELC209 MUTANT RNA RIBOZYME DOMAIN
B: P4-P6 DELC209 MUTANT RNA RIBOZYME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,20444
Polymers102,1832
Non-polymers1,02142
Water4,774265
1
A: P4-P6 DELC209 MUTANT RNA RIBOZYME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,67525
Polymers51,0911
Non-polymers58324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P4-P6 DELC209 MUTANT RNA RIBOZYME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,52919
Polymers51,0911
Non-polymers43718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.300, 125.400, 145.700
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: RNA chain P4-P6 DELC209 MUTANT RNA RIBOZYME DOMAIN


Mass: 51091.352 Da / Num. of mol.: 2 / Mutation: DELETION OF C209 / Source method: obtained synthetically
Details: The RNA was prepared by transcription with T7 RNA polymerase
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, magnesium chloride, sodium cacodylate, spermine, sodium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MgCl211
3sodium cacodylate11
4spermine11
5NaCl11
6MPD12
Crystal grow
*PLUS
Temperature: 30 ℃
Details: drop is set up using 2:8:5 ratio of solutions a, b and c
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1250 mMpotassium cacodylate1dropsolution a
2200 mM1dropsolution aMgCl2
32.5 mMspermine1dropsolution a
44 mg/mlP4-P6 RNA1dropsolution b
563 mMpotassium cacodylate1dropsolution b
613 mM1dropsolution bMgCl2
70.16 mMcobalt hexammine1dropsolution b
80.1 mMEDTA1dropsolution b
920-25 %(w/v)MPD1dropsolution c
1017 %(w/v)MPD1reservoir
11170 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 24, 1999 / Details: W16 wiggler
RadiationMonochromator: single crystal, cylindrically bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 64900 / Num. obs: 64900 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.7
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6463 / Rsym value: 57.8 / % possible all: 99.3
Reflection shell
*PLUS
% possible obs: 99.3 %

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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: 2.25→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
Details: used maximum likelihood function as implemented by CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 3017 -used the same Rfree reflection set as was used for 1gid which was then extended to include a random (10%) selection of the newly observed reflections.
Rwork0.244 ---
all-66170 --
obs-60667 91.7 %-
Displacement parametersBiso mean: 75.4 Å2
Baniso -1Baniso -2Baniso -3
1-13.601 Å20 Å20 Å2
2---31.573 Å20 Å2
3---17.972 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.45 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6741 181 126 7048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010535
X-RAY DIFFRACTIONc_angle_deg1.50534
X-RAY DIFFRACTIONc_dihedral_angle_d16.98629
X-RAY DIFFRACTIONc_improper_angle_d2.16594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
2.25-2.390.50924330.5018X-RAY DIFFRACTION83.4
2.39-2.580.44345250.4233X-RAY DIFFRACTION87.4
2.58-2.830.37234770.3475X-RAY DIFFRACTION93
2.83-3.240.28785510.2618X-RAY DIFFRACTION97.1
3.24-4.090.25825340.2278X-RAY DIFFRACTION97.8
4.09-300.20424970.1932X-RAY DIFFRACTION90.4
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0105
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.99
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.17

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