[English] 日本語
Yorodumi
- PDB-4qh3: X-ray structure of the adduct formed between bovine pancreatic ri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qh3
TitleX-ray structure of the adduct formed between bovine pancreatic ribonuclease and trans-dimethylamine methylamine dichlorido platinum(II)
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNA BINDING
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / 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
Chem-I83 / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRusso Krauss, I. / Merlino, A.
CitationJournal: Inorg.Chem. / Year: 2014
Title: Interactions between Anticancer trans-Platinum Compounds and Proteins: Crystal Structures and ESI-MS Spectra of Two Protein Adducts of trans-(Dimethylamino)(methylamino)dichloridoplatinum(II).
Authors: Messori, L. / Marzo, T. / Michelucci, E. / Russo Krauss, I. / Navarro-Ranninger, C. / Quiroga, A.G. / Merlino, A.
History
DepositionMay 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references

-
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)30,13810
Polymers27,4172
Non-polymers2,7218
Water1,58588
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0695
Polymers13,7081
Non-polymers1,3604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0695
Polymers13,7081
Non-polymers1,3604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.824, 32.537, 67.237
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-314-

HOH

21B-353-

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 (cattle) / References: UniProt: P61823, EC: 3.1.27.5
#2: Chemical
ChemComp-I83 / bis(chloranyl)-(dimethylamino)-(methylamino)platinum / trans-dimethylamine methylamine dichlorido platinum(II)


Mass: 340.109 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H10Cl2N2Pt
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG4000, 10 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
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: Jan 16, 2014
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→67.9 Å / Num. all: 14538 / Num. obs: 14538 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→67.09 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.649 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27507 734 5.1 %RANDOM
Rwork0.21406 ---
all0.21729 13780 --
obs0.21729 13780 95.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.454 Å2
Baniso -1Baniso -2Baniso -3
1--2.13 Å20 Å2-0.34 Å2
2---2.19 Å20 Å2
3---4.32 Å2
Refinement stepCycle: LAST / Resolution: 2→67.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 48 88 1968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191928
X-RAY DIFFRACTIONr_bond_other_d0.0020.021763
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9382593
X-RAY DIFFRACTIONr_angle_other_deg0.81734037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325234
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94925.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23315331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.768158
X-RAY DIFFRACTIONr_chiral_restr0.0920.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022225
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
X-RAY DIFFRACTIONr_mcbond_it3.2724.377942
X-RAY DIFFRACTIONr_mcbond_other3.2574.377941
X-RAY DIFFRACTIONr_mcangle_it4.8576.5391171
X-RAY DIFFRACTIONr_mcangle_other4.8566.5391172
X-RAY DIFFRACTIONr_scbond_it4.024.723986
X-RAY DIFFRACTIONr_scbond_other4.0184.725987
X-RAY DIFFRACTIONr_scangle_other5.5816.931422
X-RAY DIFFRACTIONr_long_range_B_refined7.85734.6422141
X-RAY DIFFRACTIONr_long_range_B_other7.85534.6592142
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 41 -
Rwork0.311 934 -
obs--86.67 %

+
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