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- PDB-1z43: Crystal structure of 7S.S SRP RNA of M. jannaschii -

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Basic information

Entry
Database: PDB / ID: 1z43
TitleCrystal structure of 7S.S SRP RNA of M. jannaschii
ComponentsRNA (101-MER)
KeywordsRNA / tetra-loop
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
Citation
Journal: Rna / Year: 2005
Title: Structural insights into SRP RNA: An induced fit mechanism for SRP assembly
Authors: Hainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
#1: Journal: Nature / Year: 2002
Title: Structure of the SRP19 RNA complex and implications for signal recognition particle assembly
Authors: Hainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
History
DepositionMar 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (101-MER)


Theoretical massNumber of molelcules
Total (without water)32,7701
Polymers32,7701
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.110, 62.110, 247.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain RNA (101-MER) / 7S.S SRP RNA / 7S SRP RNA


Mass: 32769.543 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 400, Tris buffer, sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2Tris buffer11
3sodium citrate11
4H2O11
5PEG 40012
6Tris buffer12
7sodium citrate12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.081 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 15814 / Num. obs: 15645 / % possible obs: 98.9 % / Observed criterion σ(F): 78570 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / Num. unique all: 1632 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LNG

1lng


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 18.786 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29616 783 5 %RANDOM
Rwork0.2531 ---
obs0.2552 14857 98.9 %-
all-15640 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.874 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å20 Å2
2--2.44 Å20 Å2
3----4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2169 0 139 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212427
X-RAY DIFFRACTIONr_bond_other_d0.0020.02819
X-RAY DIFFRACTIONr_angle_refined_deg3.22633787
X-RAY DIFFRACTIONr_angle_other_deg2.02432141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021061
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.320.31220
X-RAY DIFFRACTIONr_nbd_other0.360.31418
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0260.58
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.5208
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1280.510
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.38
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it2.0532427
X-RAY DIFFRACTIONr_scangle_it3.0074.53787
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.37 40
Rwork0.458 1051
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1014-2.55421.34661.9712-2.333.2089-0.01660.02380.05070.0454-0.13580.0555-0.2436-0.03540.15240.3863-0.00110.08610.3913-0.04440.318646.6659-6.8158113.3783
23.0243-1.07890.81671.1813-2.31224.25370.14380.36270.16840.0379-0.20620.12960.06070.62350.06240.3539-0.04430.04110.39350.05320.439238.73912.717896.9195
310.71752.42345.20984.393-1.71021.9753-0.08680.320.6706-0.42780.56030.81080.1144-0.6856-0.47360.30490.01770.20390.77760.11610.293520.01995.0654102.324
4-2.0784-1.42142.85852.4155-5.60274.67050.3216-0.5064-0.3469-0.96610.20970.1561.3979-0.5524-0.53120.552-0.1139-0.02250.83470.15730.65679.26475.991581.3993
54.9218-2.45012.36532.1865-2.7261.16080.0493-0.0781-0.2088-0.10920.03120.1426-0.0954-0.2693-0.08040.32490.03530.05670.4425-0.01910.433224.017516.755874.238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A138 - 147
2X-RAY DIFFRACTION1A232 - 238
3X-RAY DIFFRACTION2A182 - 197
4X-RAY DIFFRACTION2A224 - 231
5X-RAY DIFFRACTION3A148 - 152
6X-RAY DIFFRACTION3A178 - 181
7X-RAY DIFFRACTION4A153 - 177
8X-RAY DIFFRACTION5A198 - 223

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