[English] 日本語
Yorodumi
- PDB-8ub2: Structure of Adenosine monophosphate/RNase A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ub2
TitleStructure of Adenosine monophosphate/RNase A
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / RNase-A / Nucleotide Prodrug / Amino Acidyl Phosphoramidate / 5'-AMP / Phosphoramidate Hydrolysis / ProTide
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
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPallan, P.S. / Egli, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)364653263 Germany
Volkswagen FoundationAZ 92768 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Prolinyl Phosphoramidates of Nucleotides with Increased Reactivity.
Authors: Humboldt, A. / Rami, F. / Topp, F.M. / Arnold, D. / Gohringer, D. / Pallan, P.S. / Egli, M. / Richert, C.
History
DepositionSep 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

-
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)28,2948
Polymers27,4172
Non-polymers8786
Water1,874104
1
A: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2684
Polymers13,7081
Non-polymers5593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0274
Polymers13,7081
Non-polymers3183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.054, 32.514, 72.935
Angle α, β, γ (deg.)90.00, 90.81, 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 / Production host: unidentified (others) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PROTEIN WAS CRYSTALLIZED FROM 25 percent PEG 3350, 20 MM SODIUM CITRATE, PH 5.5. 5'-O-adenosine monophoshate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ligand was ...Details: PROTEIN WAS CRYSTALLIZED FROM 25 percent PEG 3350, 20 MM SODIUM CITRATE, PH 5.5. 5'-O-adenosine monophoshate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ligand was added to 2uL of reservoir solution, to achieve a concentration of ~33 mM in the soaking solution. A few RNase A crystals were soaked for 160 - 180 minutes in the soaking solution

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.3418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Sep 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 1.6→20.64 Å / Num. obs: 29170 / % possible obs: 91.9 % / Redundancy: 2.25 % / Rmerge(I) obs: 0.0835 / Net I/σ(I): 5.47
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.35 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 4826 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
APEXdata reduction
APEXdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→20.64 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.777 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26238 1371 4.7 %RANDOM
Rwork0.23682 ---
obs0.23803 27760 91.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å20.6 Å2
2---0.01 Å20 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.6→20.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 43 104 2011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121947
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161736
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6742623
X-RAY DIFFRACTIONr_angle_other_deg0.4921.5864021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2685239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.64558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23510329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022261
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02437
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_it2.3572.219965
X-RAY DIFFRACTIONr_mcbond_other2.3572.219965
X-RAY DIFFRACTIONr_mcangle_it3.5153.9781201
X-RAY DIFFRACTIONr_mcangle_other3.5143.9781202
X-RAY DIFFRACTIONr_scbond_it2.8772.555982
X-RAY DIFFRACTIONr_scbond_other2.8762.556983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.454.5311423
X-RAY DIFFRACTIONr_long_range_B_refined6.323.232133
X-RAY DIFFRACTIONr_long_range_B_other6.29923.232134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 100 -
Rwork0.301 2021 -
obs--92.5 %

+
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