[English] 日本語
Yorodumi
- PDB-4s0q: The X-ray structure of the adduct formed in the reaction between ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4s0q
TitleThe X-ray structure of the adduct formed in the reaction between bovine pancreatic ribonuclease and carboplatin
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE/RNA / ribonuclease / RNA cleavage / HYDROLASE-RNA complex
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
carboplatin / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsMerlino, A.
CitationJournal: J.Inorg.Biochem. / Year: 2015
Title: Interactions of carboplatin and oxaliplatin with proteins: Insights from X-ray structures and mass spectrometry studies of their ribonuclease A adducts.
Authors: Messori, L. / Marzo, T. / Merlino, A.
History
DepositionJan 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2015Group: Database references
Revision 1.2Feb 24, 2016Group: Database references
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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)28,1594
Polymers27,4172
Non-polymers7422
Water1,874104
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0802
Polymers13,7081
Non-polymers3711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0802
Polymers13,7081
Non-polymers3711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.521, 32.499, 72.711
Angle α, β, γ (deg.)90.00, 89.59, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 13708.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical ChemComp-QPT / carboplatin


Mass: 371.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12N2O4Pt / Comment: medication, chemotherapy*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Crystals of the RNase A-carboplatin adduct have been obtained by soaking experiments where pre-grown monoclinic protein crystals were incubated with an excess of the platinum drug (at a ...Details: Crystals of the RNase A-carboplatin adduct have been obtained by soaking experiments where pre-grown monoclinic protein crystals were incubated with an excess of the platinum drug (at a protein to platinum ratio 1:10). Crystals of RNase A were grown by hanging-drop vapor mixing 1 L of RNase A at 20 mg mL-1 with equal volumes of reservoir solution containing 20% PEG4000 and 20 mM sodium citrate buffer pH 5.0 at 298 K. Two weeks after their appearance, crystals were soaked for four days in a solution of Carboplatin dissolved in 10 L of reservoir. At the final, Pt drug:protein concentrations were in 10:1 ratio., VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→72.71 Å / Num. all: 14095 / Num. obs: 14095 / % possible obs: 99.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.124

-
Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb code 1JVT, chain A without water molecules and ligands

1jvt


Resolution: 2.09→72.71 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.663 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26175 709 5 %RANDOM
Rwork0.20518 ---
all0.20801 13380 --
obs0.20801 13380 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.837 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0 Å2-0.16 Å2
2--0.48 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.09→72.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 2 104 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191884
X-RAY DIFFRACTIONr_bond_other_d0.0010.021708
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9262542
X-RAY DIFFRACTIONr_angle_other_deg0.84633948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8955234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51125.22788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18815330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.612158
X-RAY DIFFRACTIONr_chiral_restr0.1030.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
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_it2.7443.631948
X-RAY DIFFRACTIONr_mcbond_other2.7443.631947
X-RAY DIFFRACTIONr_mcangle_it3.9915.4241178
X-RAY DIFFRACTIONr_mcangle_other3.995.4241179
X-RAY DIFFRACTIONr_scbond_it3.2193.916933
X-RAY DIFFRACTIONr_scbond_other3.2193.916933
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6565.7341364
X-RAY DIFFRACTIONr_long_range_B_refined6.46529.1362260
X-RAY DIFFRACTIONr_long_range_B_other6.45429.112233
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.093→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 55 -
Rwork0.261 909 -
obs--92.16 %

+
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