[English] 日本語
Yorodumi
- PDB-5e5e: X-ray structure of the adduct formed in the reaction between RNas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e5e
TitleX-ray structure of the adduct formed in the reaction between RNase A and a neutral organometallic derivative [Pt(pbi)(Me)(DMSO)], pbi=2-(2'-pyridil)benzimidazole (compound 3)
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
: / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.98 Å
AuthorsMerlino, A.
CitationJournal: Dalton Trans / Year: 2015
Title: Cytotoxic properties of a new organometallic platinum(ii) complex and its gold(i) heterobimetallic derivatives.
Authors: Serratrice, M. / Maiore, L. / Zucca, A. / Stoccoro, S. / Landini, I. / Mini, E. / Massai, L. / Ferraro, G. / Merlino, A. / Messori, L. / Cinellu, M.A.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease pancreatic
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8855
Polymers27,4172
Non-polymers4683
Water2,918162
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1774
Polymers13,7081
Non-polymers4683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic


Theoretical massNumber of molelcules
Total (without water)13,7081
Polymers13,7081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.398, 32.768, 72.540
Angle α, β, γ (deg.)90.00, 89.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-358-

HOH

-
Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: RNase A crystals were grown by hanging drop vapor diffusion method using a reservoir solution containing 22-24 % (w/v) PEG4K, 10 mM sodium citrate pH 5.1-5.3. The crystals are monoclinic, ...Details: RNase A crystals were grown by hanging drop vapor diffusion method using a reservoir solution containing 22-24 % (w/v) PEG4K, 10 mM sodium citrate pH 5.1-5.3. The crystals are monoclinic, space group C2, with two molecules in the asymmetric unit. The adduct was prepared by a three-days soaking in a solution that comprised the standard mother liquor used for the crystal growth to which a 2.5 mM solution of compound 3was added
PH range: 5.1-5.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→72.5 Å / Num. obs: 16494 / % possible obs: 98.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 4.8
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.408

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.98→72.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.614 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25392 834 5.1 %RANDOM
Rwork0.19182 ---
obs0.1949 15652 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.41 Å2
2---0.53 Å2-0 Å2
3---0.64 Å2
Refinement stepCycle: 1 / Resolution: 1.98→72.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1902 0 6 162 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191990
X-RAY DIFFRACTIONr_bond_other_d0.0010.021788
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9242700
X-RAY DIFFRACTIONr_angle_other_deg0.79634142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5755256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12925.27591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82415342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.997158
X-RAY DIFFRACTIONr_chiral_restr0.0950.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02462
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_it2.813.3471015
X-RAY DIFFRACTIONr_mcbond_other2.8063.3471014
X-RAY DIFFRACTIONr_mcangle_it4.3615.0111274
X-RAY DIFFRACTIONr_mcangle_other4.365.0111275
X-RAY DIFFRACTIONr_scbond_it2.7443.486975
X-RAY DIFFRACTIONr_scbond_other2.7433.488976
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2415.1131427
X-RAY DIFFRACTIONr_long_range_B_refined7.46626.292302
X-RAY DIFFRACTIONr_long_range_B_other7.42726.1552247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.985→2.036 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 49 -
Rwork0.24 1171 -
obs--96.14 %

+
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