[English] 日本語
Yorodumi
- PDB-7va3: PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7va3
TitlePaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure
Components
  • Oligoribonuclease
  • RNA (5'-R(P*GP*G)-3')
KeywordsHYDROLASE / PaOrn / Oligoribonuclease / Pseudomonas aeruginosa.
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / : / RNA / Oligoribonuclease
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, J. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870053 China
National Natural Science Foundation of China (NSFC)31800627 China
CitationJournal: To Be Published
Title: PaOrn Oligoribonuclease D11A mutant with substrate pGpG complex structure
Authors: Zhang, J. / Zhang, Q. / Bartlam, M.
History
DepositionAug 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oligoribonuclease
B: Oligoribonuclease
C: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4446
Polymers42,2653
Non-polymers1793
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-24 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.223, 83.223, 192.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Oligoribonuclease


Mass: 20809.586 Da / Num. of mol.: 2 / Mutation: D11A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: orn, PA4951 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P57665, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*GP*G)-3')


Mass: 645.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 4.01 Å3/Da / Density % sol: 69.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: 1.2M (NH4)2HPO4, 0.1M imidazole pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 60258 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 31.95 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rpim(I) all: 0.072 / Net I/σ(I): 28.44
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 2938 / CC1/2: 0.889 / CC star: 0.97 / Rpim(I) all: 0.343 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7V9Z

7v9z


Resolution: 1.8→41.61 Å / SU ML: 0.1893 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.0385
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1912 1990 3.33 %
Rwork0.1722 57847 -
obs0.1728 59837 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.95 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 46 7 261 3222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063029
X-RAY DIFFRACTIONf_angle_d0.69664111
X-RAY DIFFRACTIONf_chiral_restr0.0491452
X-RAY DIFFRACTIONf_plane_restr0.004530
X-RAY DIFFRACTIONf_dihedral_angle_d10.5583416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.35531380.32123960X-RAY DIFFRACTION95.44
1.84-1.890.27281370.28164094X-RAY DIFFRACTION98.33
1.89-1.950.27931440.25794098X-RAY DIFFRACTION98.7
1.95-2.010.25481440.22084149X-RAY DIFFRACTION99.19
2.01-2.080.22231420.20554112X-RAY DIFFRACTION98.72
2.08-2.170.23181390.18154111X-RAY DIFFRACTION99.09
2.17-2.270.19321390.17224162X-RAY DIFFRACTION99.56
2.27-2.390.18491430.15994133X-RAY DIFFRACTION99.53
2.39-2.540.20731430.17544138X-RAY DIFFRACTION99.51
2.54-2.730.20861470.18794150X-RAY DIFFRACTION99.68
2.73-3.010.22431430.1894183X-RAY DIFFRACTION99.98
3.01-3.440.18521430.17924174X-RAY DIFFRACTION99.86
3.44-4.330.17151390.14934181X-RAY DIFFRACTION99.86
4.33-41.610.15291490.14374202X-RAY DIFFRACTION99.89
Refinement TLS params.Method: refined / Origin x: 98.2861596772 Å / Origin y: 90.2662475624 Å / Origin z: 0.608556834383 Å
111213212223313233
T0.247876829834 Å20.00677061325956 Å20.00240258337392 Å2-0.430681955577 Å20.0051420553413 Å2--0.301564374222 Å2
L0.576115374318 °2-0.153762279163 °2-0.492462169122 °2-1.27618269335 °21.02370844584 °2--2.12238092992 °2
S-0.0698691679013 Å °-0.178058061346 Å °-0.00206859964223 Å °-0.0274827491243 Å °0.044107362159 Å °-0.146238222268 Å °-0.123000926319 Å °0.245998460912 Å °0.0418944881472 Å °
Refinement TLS groupSelection details: ALL

+
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