[English] 日本語
Yorodumi
- PDB-7vh4: Crystal structure of oligoribonuclease of Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vh4
TitleCrystal structure of oligoribonuclease of Escherichia coli
ComponentsOligoribonuclease
KeywordsHYDROLASE / Oligoribonuclease / ORN / RNase H-like fold / GENE REGULATION
Function / homologyRibonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / ACETATE ION / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBadhwar, P. / Taneja, B.
Funding support India, 1items
OrganizationGrant numberCountry
Not funded India
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Three-dimensional structure of a mycobacterial oligoribonuclease reveals a unique C-terminal tail that stabilizes the homodimer.
Authors: Badhwar, P. / Khan, S.H. / Taneja, B.
History
DepositionSep 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Oligoribonuclease
C: Oligoribonuclease
B: Oligoribonuclease
A: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,19513
Polymers83,7114
Non-polymers4849
Water3,261181
1
C: Oligoribonuclease
hetero molecules

D: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1518
Polymers41,8552
Non-polymers2966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
Buried area4430 Å2
ΔGint-31 kcal/mol
Surface area15770 Å2
MethodPISA
2
B: Oligoribonuclease
A: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0445
Polymers41,8552
Non-polymers1883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-20 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.574, 100.574, 147.831
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11C-61-

TRP

21B-61-

TRP

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12D
22B
13D
23A
14C
24B
15C
25A
16B
26A

NCS domain segments:

Component-ID: _ / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALADA3 - 1814 - 182
21ALAALACB3 - 1814 - 182
12ALAALADA3 - 1814 - 182
22ALAALABC3 - 1814 - 182
13ALAALADA3 - 1814 - 182
23ALAALAAD3 - 1814 - 182
14ALAALACB3 - 1814 - 182
24ALAALABC3 - 1814 - 182
15ALAALACB3 - 1814 - 182
25ALAALAAD3 - 1814 - 182
16SERSERBC2 - 1813 - 182
26SERSERAD2 - 1813 - 182

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules DCBA

#1: Protein
Oligoribonuclease


Mass: 20927.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: orn / Plasmid: pET28a-His10-Smt3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6D2W9V9, EC: 3.1.13.3

-
Non-polymers , 5 types, 190 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.26 % / Description: thin, flat, sheet-like
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Sodium HEPES, pH 7.5, 0.25 M Sodium acetate, 25 % v/v PEG-3350
PH range: 7-8

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.3→59.63 Å / Num. obs: 34389 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 54.922 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.043 / Rrim(I) all: 0.086 / Χ2: 0.98 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3274 / Rpim(I) all: 0.299 / Rrim(I) all: 0.615 / % possible all: 98.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IGI

2igi


Resolution: 2.3→59.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 8.886 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.381 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1673 4.9 %RANDOM
Rwork0.1938 ---
obs0.1963 32650 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.25 Å2 / Biso mean: 55.092 Å2 / Biso min: 26.49 Å2
Baniso -1Baniso -2Baniso -3
1--2.77 Å20 Å20 Å2
2---2.77 Å20 Å2
3---5.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5705 0 30 181 5916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135964
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175555
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.6448082
X-RAY DIFFRACTIONr_angle_other_deg1.2711.57812853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15621.749366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.907151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5491555
X-RAY DIFFRACTIONr_chiral_restr0.0650.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026657
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021316
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D59160.05
12C59160.05
21D58530.07
22B58530.07
31D58430.06
32A58430.06
41C58600.07
42B58600.07
51C58850.06
52A58850.06
61B59600.06
62A59600.06
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 130 -
Rwork0.298 2314 -
all-2444 -
obs--98 %

+
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