[English] 日本語
Yorodumi
- PDB-7v5h: VcOrn native structure with N terminal tag -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v5h
TitleVcOrn native structure with N terminal tag
ComponentsOligoribonuclease
KeywordsHYDROLASE / VcOrn / Active pocket / N terminal tag.
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
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, J. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800627 China
National Natural Science Foundation of China (NSFC)31870053 China
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of oligoribonuclease from Vibrio cholerae O1 El Tor with bound peptide.
Authors: Zhang, J. / Sun, L. / Zhang, Q. / Bartlam, M.
History
DepositionAug 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oligoribonuclease


Theoretical massNumber of molelcules
Total (without water)22,7121
Polymers22,7121
Non-polymers00
Water2,666148
1
A: Oligoribonuclease

A: Oligoribonuclease


Theoretical massNumber of molelcules
Total (without water)45,4232
Polymers45,4232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area4680 Å2
ΔGint-26 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.522, 84.522, 55.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein Oligoribonuclease


Mass: 22711.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Gene: orn, VC_0341 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9KV17, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 2.0M sodium formate, 0.1M sodium acetate trihydrate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 25735 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 23.04 Å2 / Rpim(I) all: 0.041 / Net I/σ(I): 25.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 2.76 / Num. unique obs: 1259 / Rpim(I) all: 0.395 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N6A

6n6a


Resolution: 1.7→27.67 Å / SU ML: 0.1525 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 20.3454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1926 1917 7.71 %
Rwork0.1732 22946 -
obs0.1748 24863 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 0 148 1672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721558
X-RAY DIFFRACTIONf_angle_d0.96712105
X-RAY DIFFRACTIONf_chiral_restr0.0634231
X-RAY DIFFRACTIONf_plane_restr0.0075269
X-RAY DIFFRACTIONf_dihedral_angle_d6.1826201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.29731230.22541508X-RAY DIFFRACTION89.52
1.74-1.790.22131290.19941529X-RAY DIFFRACTION91.4
1.79-1.840.23371270.20531551X-RAY DIFFRACTION91.95
1.84-1.90.23751280.1971555X-RAY DIFFRACTION93.6
1.9-1.970.22881340.1851611X-RAY DIFFRACTION95.72
1.97-2.050.20491400.17071628X-RAY DIFFRACTION97.57
2.05-2.140.18861300.16541651X-RAY DIFFRACTION98.29
2.14-2.250.19421440.1631666X-RAY DIFFRACTION98.53
2.25-2.390.19021410.17391655X-RAY DIFFRACTION98.63
2.39-2.580.20231410.17631678X-RAY DIFFRACTION98.91
2.58-2.840.22051390.19581688X-RAY DIFFRACTION99.46
2.84-3.250.1891450.16971720X-RAY DIFFRACTION99.89
3.25-4.090.16921460.16251710X-RAY DIFFRACTION100
4.09-27.670.17681500.16471796X-RAY DIFFRACTION99.59
Refinement TLS params.Method: refined / Origin x: 57.3275569127 Å / Origin y: 35.3102681131 Å / Origin z: 8.50648304712 Å
111213212223313233
T0.140033589068 Å2-0.0210632476841 Å2-0.00897136378163 Å2-0.177413873276 Å20.00230860218918 Å2--0.159429222635 Å2
L0.965813045788 °2-0.063737947679 °20.0161922732766 °2-1.1433496665 °20.00163995294456 °2--1.48908405056 °2
S-0.0403472992183 Å °-0.0677815467609 Å °-0.0670391256364 Å °-0.0137690551093 Å °0.0210329010324 Å °-0.0605391913528 Å °0.0581966011081 Å °0.0129910274414 Å °0.02452284342 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