[English] 日本語
Yorodumi
- PDB-6cc3: Crystal structure of ykoY-mntP riboswitch chimera bound to cadmium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cc3
TitleCrystal structure of ykoY-mntP riboswitch chimera bound to cadmium
ComponentsRNA (101-MER)
KeywordsRNA / Riboswitch / yybP-ykoY
Function / homology: / GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.698 Å
AuthorsBachas, S. / Ferre-D'amare, A.R.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.
Authors: Bachas, S.T. / Ferre-D'Amare, A.R.
History
DepositionFeb 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (101-MER)
B: RNA (101-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,12932
Polymers65,3452
Non-polymers2,78430
Water81145
1
A: RNA (101-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,25020
Polymers32,6731
Non-polymers1,57719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA (101-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,87912
Polymers32,6731
Non-polymers1,20711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.531, 68.288, 83.384
Angle α, β, γ (deg.)90.00, 97.96, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: RNA chain RNA (101-MER)


Mass: 32672.500 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 100 mM Magnesium Formate, 15% PEG 3350, 5mM Cadmium Chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.698→50 Å / Num. obs: 19403 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.63
Reflection shellResolution: 2.698→2.75 Å / Rmerge(I) obs: 0.802 / Num. unique obs: 877

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4y1i

4y1i


Resolution: 2.698→46.658 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2485 1916 9.99 %
Rwork0.1958 --
obs0.2011 19173 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.698→46.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 4114 92 45 4251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024676
X-RAY DIFFRACTIONf_angle_d0.5137284
X-RAY DIFFRACTIONf_dihedral_angle_d13.9022323
X-RAY DIFFRACTIONf_chiral_restr0.026968
X-RAY DIFFRACTIONf_plane_restr0.003194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6983-2.76580.43051260.39731132X-RAY DIFFRACTION91
2.7658-2.84050.40031320.35751179X-RAY DIFFRACTION95
2.8405-2.92410.36241330.29711205X-RAY DIFFRACTION99
2.9241-3.01850.29811360.25361223X-RAY DIFFRACTION99
3.0185-3.12630.28811420.23531267X-RAY DIFFRACTION100
3.1263-3.25150.2561360.21641242X-RAY DIFFRACTION100
3.2515-3.39940.28161350.19761230X-RAY DIFFRACTION99
3.3994-3.57860.2561370.18981232X-RAY DIFFRACTION100
3.5786-3.80270.24611380.181250X-RAY DIFFRACTION99
3.8027-4.09610.22991370.16341228X-RAY DIFFRACTION100
4.0961-4.5080.20511400.15011260X-RAY DIFFRACTION100
4.508-5.15960.19681410.15541266X-RAY DIFFRACTION100
5.1596-6.49780.20311390.17461258X-RAY DIFFRACTION100
6.4978-46.66480.24231440.19211285X-RAY DIFFRACTION99
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)
14.33610.86621.56791.10261.0110.9966-0.08030.01050.0912-0.16140.06790.3246-0.0084-0.25010.05650.3746-0.1573-0.00380.72790.03510.512228.7236-6.779121.8418
25.64312.1439-0.01732.60940.52070.0462-0.0204-0.34250.104-0.1788-0.13590.0157-0.0621-0.23910.13550.3546-0.0914-0.00580.58010.02270.374917.668-20.683925.9236
30.59231.0495-0.10781.80980.55874.4793-0.2310.0444-0.1374-0.1979-0.00640.29470.1259-0.17850.17520.3021-0.0120.00390.5591-0.11670.512342.1062-0.581140.4958
47.11122.0614-1.12172.55831.32665.449-0.17-0.4152-0.2432-0.1395-0.18250.1061-0.0988-0.40670.30710.5935-0.0281-0.28970.48110.10750.75196.5979-4.91127.0502
54.88832.9314-3.84372.0899-2.11595.2424-0.4260.245-0.554-0.56640.05170.22320.4286-0.03350.42620.5731-0.01680.12440.8292-0.05490.662738.5434-26.83937.4112
63.8654-0.2157-1.15865.3849-1.34945.90420.1044-0.425-0.2458-0.2415-0.4184-0.13540.54550.43170.32660.4324-0.07460.08770.7084-0.01850.413255.914-15.686313.4515
75.8601-1.714.53211.9984-3.2817.3791.5317-0.6332-0.73643.06870.8778-0.54921.0558-0.0008-2.01964.92740.20030.17181.39960.23712.64457.1034-43.2827.5869
85.4016-0.1281-0.23425.36710.06332.5375-0.63020.5277-0.2006-1.33250.06060.44940.2718-0.06980.61520.8918-0.0770.03470.9223-0.23880.642445.3134-23.3017-4.1872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:35)
2X-RAY DIFFRACTION2(chain A and resid 36:71)
3X-RAY DIFFRACTION3(chain A and resid 72:91)
4X-RAY DIFFRACTION4(chain A and resid 92:102)
5X-RAY DIFFRACTION5(chain B and resid 3:28)
6X-RAY DIFFRACTION6(chain B and resid 29:74)
7X-RAY DIFFRACTION7(chain B and resid 82:85)
8X-RAY DIFFRACTION8(chain B and resid 86:101)

+
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://pdbjlc1.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