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- PDB-1d4r: 29-mer fragment of human srp rna helix 6 -

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Basic information

Entry
Database: PDB / ID: 1d4r
Title29-mer fragment of human srp rna helix 6
Components(29-MER OF MODIFIED SRP RNA HELIX 6) x 2
KeywordsRNA / A-RNA HELIX / GGAG/GAGG BULGE / AC/CA TANDEM MISMATCH / GU WOBBLE BASE PAIRS / 2'3' -CYCLIC PHOSPHATE
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWild, K. / Weichenrieder, O. / Leonard, G.A. / Cusack, S.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The 2 A structure of helix 6 of the human signal recognition particle RNA
Authors: Wild, K. / Weichenrieder, O. / Leonard, G.A. / Cusack, S.
History
DepositionOct 5, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_conn_type / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_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_conn.ptnr2_symmetry / _struct_conn_type.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

Downloads & links

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Assembly

Deposited unit
A: 29-MER OF MODIFIED SRP RNA HELIX 6
B: 29-MER OF MODIFIED SRP RNA HELIX 6
C: 29-MER OF MODIFIED SRP RNA HELIX 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6498
Polymers28,5283
Non-polymers1225
Water2,198122
1
A: 29-MER OF MODIFIED SRP RNA HELIX 6
B: 29-MER OF MODIFIED SRP RNA HELIX 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1366
Polymers19,0392
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 29-MER OF MODIFIED SRP RNA HELIX 6
hetero molecules

C: 29-MER OF MODIFIED SRP RNA HELIX 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0264
Polymers18,9772
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)42.980, 42.980, 231.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: RNA chain 29-MER OF MODIFIED SRP RNA HELIX 6


Mass: 9550.621 Da / Num. of mol.: 1 / Fragment: NON-NATIVE DUPLEX / Mutation: C28U / Source method: obtained synthetically
Details: THE RNA WAS PRODUCED BY T7 RNA POLYMERASE IN VITRO TRANSCRIPTION USING RIBOZYME TECHNOLOGY. THIS SEQUENCE OCCURS NATURALLY IN HUMANS
#2: RNA chain 29-MER OF MODIFIED SRP RNA HELIX 6


Mass: 9488.656 Da / Num. of mol.: 2 / Fragment: NON-NATIVE DUPLEX / Mutation: C28U / Source method: obtained synthetically
Details: THE RNA WAS PRODUCED BY T7 RNA POLYMERASE IN VITRO TRANSCRIPTION USING RIBOZYME TECHNOLOGY. THIS SEQUENCE OCCURS NATURALLY IN HUMANS
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 MM MGCL2, 1 MM SPERMINE TETRAHYDROCHLORIDE, 50 MM MES, 15-20% (W/V) PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2SPERMINE TETRAHYDROCHLORIDE11
3MES11
4PEG 800011
5PEG 800012
6MGCL212
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM1reservoirMgCl2
250 mMMES1reservoir
315-20 %(w/v)PEG80001reservoir
41
51

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 7, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→76 Å / Num. all: 17877 / Num. obs: 17877 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 6.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.398 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 76 Å
Reflection shell
*PLUS
% possible obs: 100 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
SOLVEphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 2→38.57 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 929754.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: NO RESTRAINTS WERE USED FOR NCS OR RNA GEOMETRY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 859 4.8 %RANDOM
Rwork0.264 ---
all0.275 17808 --
obs0.264 17808 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.59 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 59.4 Å2
Baniso -1Baniso -2Baniso -3
1-8.72 Å21.23 Å20 Å2
2--8.72 Å20 Å2
3----17.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2030 25 122 2177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.92
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d0
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.54
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.457 144 5 %
Rwork0.403 2756 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA-ALLATOM-MOD.PARAMDNA-RNA-ALLATOM-MOD.TOP
X-RAY DIFFRACTION2MG-MOD.PARAMMG-MOD.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg0
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.54

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