[English] 日本語
Yorodumi
- PDB-1p79: Crystal structure of a bulged RNA tetraplex: implications for a n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p79
TitleCrystal structure of a bulged RNA tetraplex: implications for a novel binding site in RNA tetraplex
Components5'-R(*UP*GP*UP*GP*GP*U)-3'
KeywordsRNA / TETRAPLEX / BULGE
Function / homology: / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.1 Å
AuthorsPan, B. / Xiong, Y. / Shi, K. / Sundaralingam, M.
CitationJournal: STRUCTURE / Year: 2003
Title: Crystal Structure of a Bulged RNA Tetraplex at 1.1 A Resolution: Implications for a Novel Binding Site in RNA Tetraplex
Authors: Pan, B. / Xiong, Y. / Shi, K. / Sundaralingam, M.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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_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_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.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.ptnr1_symmetry / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-R(*UP*GP*UP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,0264
Polymers1,9091
Non-polymers1173
Water54030
1
A: 5'-R(*UP*GP*UP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*GP*UP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*GP*UP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*GP*UP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,10616
Polymers7,6374
Non-polymers46912
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation6_556x+1/2,-y+1/2,-z+11
crystal symmetry operation3_555-y+1/2,x+1/2,z1
Unit cell
Length a, b, c (Å)35.014, 35.014, 22.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-201-

K

21A-202-

K

31A-203-

K

41A-115-

HOH

-
Components

#1: RNA chain 5'-R(*UP*GP*UP*GP*GP*U)-3'


Mass: 1909.157 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 31.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: spermine, potassium chloride, MPD, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1spermine11
2potassium chloride11
3MPD11
4cacodylate11
5potassium chloride12
6MPD12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mMsodium cacodylate1droppH6.0
212 mMspermine tetrahydrochloride1drop
380 mM1dropKCl
410 %(v/v)MPD1drop
550 mM1dropKCl
610 %1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.8985 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 20, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8985 Å / Relative weight: 1
ReflectionResolution: 1.1→16.55 Å / Num. obs: 5690 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20 % / Rsym value: 0.037 / Net I/σ(I): 23
Reflection shellResolution: 1.1→1.14 Å / Num. unique all: 770 / Rsym value: 0.088 / % possible all: 71.9
Reflection
*PLUS
Highest resolution: 1.1 Å / Num. obs: 10280 / Num. measured all: 206863 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 71.9 % / Rmerge(I) obs: 0.088

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.1→16.55 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.242 / SU ML: 0.013 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.027 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: extra hydrogen on G 2 of chain A was removed. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.13607 308 5.4 %RANDOM
Rwork0.12678 ---
obs0.12733 5382 94.82 %-
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: 6.497 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.1→16.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 162 3 90 255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021120
X-RAY DIFFRACTIONr_bond_other_d0.0030.0243
X-RAY DIFFRACTIONr_angle_refined_deg1.6073185
X-RAY DIFFRACTIONr_angle_other_deg2.0983111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.219
X-RAY DIFFRACTIONr_gen_planes_refined0.0320.0254
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.4120.224
X-RAY DIFFRACTIONr_nbd_other0.1960.239
X-RAY DIFFRACTIONr_nbtor_other0.0960.229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.7520.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3460.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it1.5393120
X-RAY DIFFRACTIONr_scangle_it2.0654.5185
X-RAY DIFFRACTIONr_rigid_bond_restr0.8552120
X-RAY DIFFRACTIONr_sphericity_free8.627534
X-RAY DIFFRACTIONr_sphericity_bonded2.6735108
LS refinement shellResolution: 1.1→1.16 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.11 34
Rwork0.08 589
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)
14.5167-7.7103-1.678113.36561.61892.9291-0.2282-0.0859-0.18320.46050.04970.2770.06530.03040.17850.0361-0.00590.01320.03240.0060.0366-0.098210.335315.1683
20.48390.4766-2.7451-0.39910.20262.7114-0.0288-0.1647-0.09580.01040.0519-0.0009-0.02170.1488-0.02310.020.01180.00230.03560.01020.05165.61928.176410.4529
30.263-1.12721.03953.50810.91041.81020.0626-0.0562-0.16620.0358-0.01060.0311-0.0097-0.0711-0.05190.0283-0.0045-0.00020.02540.00630.049-1.679510.31749.7291
41.9688-1.15061.03953.0488-0.63420.8431-0.01570.1175-0.1307-0.05340.08950.1638-0.02460.0263-0.07380.0324-0.0015-0.00550.0291-0.00960.0385-4.786611.72486.1916
56.26753.1361-0.63111.4096-2.3331.2765-0.02910.306-0.2125-0.3654-0.0874-0.2060.0642-0.00480.11660.0475-0.0039-0.00040.0392-0.03010.0233-2.416310.89622.7258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22
2X-RAY DIFFRACTION2AA33
3X-RAY DIFFRACTION3AA44
4X-RAY DIFFRACTION4AA55
5X-RAY DIFFRACTION5AA66
Refinement
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.136 / Rfactor Rwork: 0.127
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more