[English] 日本語
Yorodumi
- PDB-6ck4: G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ck4
TitleG96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp
ComponentsPRPP riboswitch
KeywordsRNA / Riboswitch / ykkC / PRPP / ppGpp
Function / homologyGUANOSINE-5',3'-TETRAPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / : / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesThermoanaerobacter mathranii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.097 Å
AuthorsReiss, C.W. / Knappenberger, A.J. / Strobel, S.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM022778 United States
CitationJournal: Elife / Year: 2018
Title: Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA.
Authors: Knappenberger, A.J. / Reiss, C.W. / Strobel, S.A.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PRPP riboswitch
B: PRPP riboswitch
C: PRPP riboswitch
D: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,11449
Polymers150,7134
Non-polymers4,40145
Water37821
1
A: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,22915
Polymers37,6781
Non-polymers1,55114
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5119
Polymers37,6781
Non-polymers8328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,73113
Polymers37,6781
Non-polymers1,05312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: PRPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,64312
Polymers37,6781
Non-polymers96511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.252, 62.147, 125.909
Angle α, β, γ (deg.)91.180, 89.610, 101.940
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name P or name...
21(chain B and ((resid 1 and (name P or name...
31(chain C and ((resid 1 and (name P or name...
41(chain D and (resid 1 through 37 or (resid 38...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 1 and (name P or name...A1
121(chain A and ((resid 1 and (name P or name...A0 - 112
131(chain A and ((resid 1 and (name P or name...A0 - 112
141(chain A and ((resid 1 and (name P or name...A0 - 112
151(chain A and ((resid 1 and (name P or name...A0 - 112
161(chain A and ((resid 1 and (name P or name...A0 - 112
171(chain A and ((resid 1 and (name P or name...A0 - 112
181(chain A and ((resid 1 and (name P or name...A0 - 112
191(chain A and ((resid 1 and (name P or name...A0 - 112
1101(chain A and ((resid 1 and (name P or name...A0 - 112
1111(chain A and ((resid 1 and (name P or name...A0 - 112
1121(chain A and ((resid 1 and (name P or name...A0 - 112
211(chain B and ((resid 1 and (name P or name...B1
221(chain B and ((resid 1 and (name P or name...B0 - 111
231(chain B and ((resid 1 and (name P or name...B0 - 111
241(chain B and ((resid 1 and (name P or name...B0 - 111
251(chain B and ((resid 1 and (name P or name...B0 - 111
261(chain B and ((resid 1 and (name P or name...B0 - 111
271(chain B and ((resid 1 and (name P or name...B0 - 111
281(chain B and ((resid 1 and (name P or name...B0 - 111
291(chain B and ((resid 1 and (name P or name...B0 - 111
2101(chain B and ((resid 1 and (name P or name...B0 - 111
2111(chain B and ((resid 1 and (name P or name...B0 - 111
2121(chain B and ((resid 1 and (name P or name...B0 - 111
311(chain C and ((resid 1 and (name P or name...C1
321(chain C and ((resid 1 and (name P or name...C0 - 111
331(chain C and ((resid 1 and (name P or name...C0 - 111
341(chain C and ((resid 1 and (name P or name...C0 - 111
351(chain C and ((resid 1 and (name P or name...C0 - 111
361(chain C and ((resid 1 and (name P or name...C0 - 111
371(chain C and ((resid 1 and (name P or name...C0 - 111
381(chain C and ((resid 1 and (name P or name...C0 - 111
391(chain C and ((resid 1 and (name P or name...C0 - 111
3101(chain C and ((resid 1 and (name P or name...C0 - 111
3111(chain C and ((resid 1 and (name P or name...C0 - 111
3121(chain C and ((resid 1 and (name P or name...C0 - 111
411(chain D and (resid 1 through 37 or (resid 38...D1 - 37
421(chain D and (resid 1 through 37 or (resid 38...D38
431(chain D and (resid 1 through 37 or (resid 38...D0 - 115
441(chain D and (resid 1 through 37 or (resid 38...D0 - 115
451(chain D and (resid 1 through 37 or (resid 38...D0 - 115
461(chain D and (resid 1 through 37 or (resid 38...D0 - 115
471(chain D and (resid 1 through 37 or (resid 38...D0 - 115
481(chain D and (resid 1 through 37 or (resid 38...D0 - 115
491(chain D and (resid 1 through 37 or (resid 38...D0 - 115
4101(chain D and (resid 1 through 37 or (resid 38...D0 - 115
4111(chain D and (resid 1 through 37 or (resid 38...D0 - 115
4121(chain D and (resid 1 through 37 or (resid 38...D0 - 115
4131(chain D and (resid 1 through 37 or (resid 38...D0 - 115

-
Components

-
RNA chain , 1 types, 4 molecules ABCD

#1: RNA chain
PRPP riboswitch


Mass: 37678.297 Da / Num. of mol.: 4 / Fragment: GB residues 657680-657796 / Mutation: G96A / Source method: obtained synthetically / Source: (synth.) Thermoanaerobacter mathranii (bacteria) / References: GenBank: 296841273

-
Non-polymers , 6 types, 66 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical...
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: K
#5: Chemical
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.7 Å3/Da / Density % sol: 54.47 % / Description: Crystals formed as thin plates.
Crystal growTemperature: 296.15 K / Method: microbatch / pH: 7.5
Details: 1 uL 150 uM RNA in 10 mM magnesium chloride, 10 mM potassium chloride, 10 mM HEPES-KOH, pH 7.5, 1 mM ppGpp, mixed with 0.8 uL 80 mM sodium chloride, 40 mM sodium cacodylate, pH 7.0, 30% MPD, 12 mM spermine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2017
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.097→40 Å / Num. obs: 26741 / % possible obs: 93.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 97.77 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.082 / Rrim(I) all: 0.13 / Χ2: 0.927 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.152.11.22213090.2531.0261.6040.91294.7
3.15-3.212.31.13313420.3650.951.4870.95194.3
3.21-3.272.31.1213560.2980.9391.471.00794.6
3.27-3.342.41.06213640.4990.8811.3881.00494.7
3.34-3.412.30.90513410.5780.7521.1831.01795.3
3.41-3.492.30.92913860.4610.7791.2190.98594.5
3.49-3.582.30.79513620.6060.6651.0421.05695.7
3.58-3.682.20.75313430.6730.6380.9921.01594.5
3.68-3.782.20.62313500.8230.5220.8180.91394.7
3.78-3.912.20.60113410.7550.5060.790.98993
3.91-4.042.20.61213300.7720.5130.8030.97893.5
4.04-4.212.10.5113170.7410.430.6710.9892.9
4.21-4.420.41512630.7730.3470.5450.93487.6
4.4-4.632.10.27811980.8940.2340.3660.90285.1
4.63-4.922.30.2313780.8770.1910.3010.87895.8
4.92-5.32.40.14413850.9490.120.1890.87596.3
5.3-5.832.30.10513750.9730.0870.1370.90395.8
5.83-6.672.30.07513770.9870.0620.0980.8695.8
6.67-8.392.10.0412920.9960.0330.0520.71991
8.39-402.30.03213320.9920.0260.0420.64393.2

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å36.54 Å
Translation3.1 Å36.54 Å

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.7.17phasing
PHENIX1.12-2829refinement
REFMAC5refinement
PDB_EXTRACT3.24data extraction
Cootmodel building
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.097→36.539 Å / SU ML: 0.64 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 43.12
RfactorNum. reflection% reflection
Rfree0.3041 1263 4.74 %
Rwork0.2484 --
obs0.2509 26642 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 352.48 Å2 / Biso mean: 144.6331 Å2 / Biso min: 34.84 Å2
Refinement stepCycle: final / Resolution: 3.097→36.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 8829 191 21 9041
Biso mean--120.91 95.64 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01810075
X-RAY DIFFRACTIONf_angle_d1.85215597
X-RAY DIFFRACTIONf_chiral_restr0.1372082
X-RAY DIFFRACTIONf_plane_restr0.01412
X-RAY DIFFRACTIONf_dihedral_angle_d19.5565005
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4438X-RAY DIFFRACTION10.364TORSIONAL
12B4438X-RAY DIFFRACTION10.364TORSIONAL
13C4438X-RAY DIFFRACTION10.364TORSIONAL
14D4438X-RAY DIFFRACTION10.364TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0965-3.22050.42851250.41222671279689
3.2205-3.36690.44071410.41032882302394
3.3669-3.54430.42051400.3942895303595
3.5443-3.76620.40071770.35882826300394
3.7662-4.05660.40951460.3262843298993
4.0566-4.46420.33481250.28692696282189
4.4642-5.10870.30351220.22262833295593
5.1087-6.43070.25561440.2052922306696
6.4307-36.54190.23231430.17592811295492

+
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://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