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- PDB-1gid: CRYSTAL STRUCTURE OF A GROUP I RIBOZYME DOMAIN: PRINCIPLES OF RNA... -

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Basic information

Entry
Database: PDB / ID: 1gid
TitleCRYSTAL STRUCTURE OF A GROUP I RIBOZYME DOMAIN: PRINCIPLES OF RNA PACKING
ComponentsP4-P6 RNA RIBOZYME DOMAIN
KeywordsRIBOZYME / RNA / P4-P6 RIBOZYME DOMAIN OF THE TETRAHYMENA GROUP I INTRON
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD-SIR / Resolution: 2.5 Å
AuthorsCate, J.H. / Gooding, A.R. / Podell, E. / Zhou, K. / Golden, B.L. / Kundrot, C.E. / Cech, T.R. / Doudna, J.A.
Citation
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. / Doudna, J.A.
#1: Journal: Science / Year: 1996
Title: RNA Tertiary Structure Mediation by Adenosine
Authors: Cate, J.H. / Gooding, A.R. / Podell, E. / Zhou, K. / Golden, B.L. / Szewczak, A.A. / Kundrot, C.E. / Cech, T.R. / Doudna, J.A.
#2: Journal: Structure / Year: 1996
Title: Metal-Binding Sites in the Major Groove of a Large Ribozyme Domain
Authors: Cate, J.H. / Doudna, J.A.
History
DepositionAug 22, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 31, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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
Remark 999SEQUENCE REFERENCE: MURPHY, F.L., CECH, T.R. BIOCHEMISTRY 32, 5291 (1993).

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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)103,33030
Polymers102,1032
Non-polymers1,22828
Water1086
1
A: P4-P6 RNA RIBOZYME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66515
Polymers51,0511
Non-polymers61414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P4-P6 RNA RIBOZYME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66515
Polymers51,0511
Non-polymers61414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.800, 128.700, 145.900
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 RNA RIBOZYME DOMAIN


Mass: 51051.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: T7 TRANSCRIPT / Source: (natural) synthetic construct (others)
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.3 Å3/Da / Density % sol: 71 %
Crystal growMethod: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2K CACODYLATE11
3MGCL211
4SPERMINE11
5[CO(NH3)6]CL311
6WATER12
7MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 mMpotassium cacodylate1reservoir
230 mMmagnesium chloride1reservoir
30.3 mMspermine1reservoir
40.2-1.0 mMcobalt hexammine chloride1reservoir
5methylpentanediol1reservoir
61
71

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: CCD / Date: Dec 30, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→18 Å / Num. obs: 36401 / % possible obs: 73 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.043 / Net I/σ(I): 23.7
Reflection shellResolution: 2.77→2.86 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.264 / % possible all: 80.2

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Processing

Software
NameVersionClassification
MAD-SIRmodel building
X-PLOR3.843refinement
DENZOdata reduction
CCP4data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD-SIR / Resolution: 2.5→8 Å / Cross valid method: FREE R / σ(F): 2
Details: NUCLEIC ACID RNA-DNA PARAMETER FILE: G. PARKINSON,ET AL. (1996) ACTA CRYST. D52, 57-64
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1788 5.4 %RANDOM
Rwork0.242 ---
obs0.242 35100 73.5 %-
Displacement parametersBiso mean: 45 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6766 52 6 6824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.27
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d13.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.78
X-RAY DIFFRACTIONx_mcangle_it5.87
X-RAY DIFFRACTIONx_scbond_it2.98
X-RAY DIFFRACTIONx_scangle_it4.59
Refine LS restraints NCSNCS model details: 14 GROUPS
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.51 72 5 %
Rwork0.398 1368 -
obs--60.3 %
Xplor fileSerial no: 2 / Param file: DNA-RNA-MULTI-ENDO.PARAM / Topol file: DNA-RNA-MULTI-ENDO.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg13.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
X-RAY DIFFRACTIONx_mcbond_it3.78
X-RAY DIFFRACTIONx_scbond_it2.98
X-RAY DIFFRACTIONx_mcangle_it5.87
X-RAY DIFFRACTIONx_scangle_it4.59
LS refinement shell
*PLUS
Rfactor Rfree: 0.51 / % reflection Rfree: 5 % / Total num. of bins used: 20

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