[English] 日本語
Yorodumi
- PDB-5dar: CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dar
TitleCRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII
Components
  • (50S ribosomal protein ...) x 2
  • 74 nt fragment of 23S rRNA
KeywordsRIBOSOMAL PROTEIN / ribosome / P-stalk / archaea
Function / homology
Function and homology information


large ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal protein L10, N-terminal fragment, domain II / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Molybdopterin biosynthesis moea protein, domain 2 / 50S ribosomal protein L10, archaea / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P ...Ribosomal protein L10, N-terminal fragment, domain II / Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Molybdopterin biosynthesis moea protein, domain 2 / 50S ribosomal protein L10, archaea / : / 50S ribosomal protein L10, insertion domain superfamily / 60S ribosomal protein L10P, insertion domain / Insertion domain in 60S ribosomal protein L10P / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B.
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF THE BASE OF THE RIBOSOMAL P STALK FROM METHANOCOCCUS JANNASCHII
Authors: Gabdulkhakov, A.G. / Mitroshin, I.V. / Garber, M.B.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 74 nt fragment of 23S rRNA
B: 50S ribosomal protein L10
C: 50S ribosomal protein L11
D: 74 nt fragment of 23S rRNA
E: 50S ribosomal protein L10
F: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,08722
Polymers129,5916
Non-polymers49616
Water25214
1
A: 74 nt fragment of 23S rRNA
B: 50S ribosomal protein L10
C: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,10513
Polymers64,7953
Non-polymers31010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-114 kcal/mol
Surface area24400 Å2
MethodPISA
2
D: 74 nt fragment of 23S rRNA
E: 50S ribosomal protein L10
F: 50S ribosomal protein L11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9829
Polymers64,7953
Non-polymers1876
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-84 kcal/mol
Surface area25680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.396, 88.451, 95.231
Angle α, β, γ (deg.)90.00, 102.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
RNA chain , 1 types, 2 molecules AD

#1: RNA chain 74 nt fragment of 23S rRNA


Mass: 23928.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pMja23S-74.UC18 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): XL1(Blue) / References: GenBank: 470491724

-
50S ribosomal protein ... , 2 types, 4 molecules BECF

#2: Protein 50S ribosomal protein L10 / Acidic ribosomal protein P0 homolog / MjaL10


Mass: 23353.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpl10, rplP0, MJ0509 / Plasmid: pET-11c/MjaP0NTF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54049
#3: Protein 50S ribosomal protein L11


Mass: 17513.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: rpl11, MJ0373 / Plasmid: pET-11c/MjaL11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pUBS520 / References: UniProt: P54030

-
Non-polymers , 4 types, 30 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Tris-HCl, pH 7.5, 0.15 M KCl, 20 mM MgCl2, 15% PEG 4000

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. all: 25542 / Num. obs: 25542 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Redundancy: 4.35 % / Rsym value: 0.14 / Net I/σ(I): 7.01
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.09 / % possible all: 96.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5COL, 5D6G

5col

5d6g


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.812 / Cross valid method: THROUGHOUT / ESU R Free: 0.521 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29679 1293 5.1 %RANDOM
Rwork0.26443 ---
obs0.26607 24191 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å2-0 Å2-1.58 Å2
2---0.14 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 3176 16 14 8414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0168832
X-RAY DIFFRACTIONr_bond_other_d0.0010.026967
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.69212666
X-RAY DIFFRACTIONr_angle_other_deg3.374316312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7095674
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88125.989182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.581151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7031522
X-RAY DIFFRACTIONr_chiral_restr0.1020.21448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217473
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021725
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6685.5512717
X-RAY DIFFRACTIONr_mcbond_other3.6675.552716
X-RAY DIFFRACTIONr_mcangle_it6.3348.3063384
X-RAY DIFFRACTIONr_mcangle_other6.3338.3073385
X-RAY DIFFRACTIONr_scbond_it1.9943.4776115
X-RAY DIFFRACTIONr_scbond_other1.9943.4776116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4575.1359283
X-RAY DIFFRACTIONr_long_range_B_refined9.66635.56739239
X-RAY DIFFRACTIONr_long_range_B_other9.65635.57339221
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 107 -
Rwork0.361 1714 -
obs--96.6 %

+
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://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