[English] 日本語
Yorodumi
- PDB-7vsa: E. coli Ribonuclease HI in complex with two Mg2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vsa
TitleE. coli Ribonuclease HI in complex with two Mg2+
ComponentsRibonuclease HI
KeywordsHYDROLASE / endonuclease / metalloenzyme
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm
Similarity search - Function
Ribonuclease HI / : / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLiao, Z. / Oyama, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H02120 Japan
Japan Science and TechnologyJPMJTM20NM Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography.
Authors: Liao, Z. / Oyama, T. / Kitagawa, Y. / Katayanagi, K. / Morikawa, K. / Oda, M.
History
DepositionOct 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 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: Ribonuclease HI
B: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,81611
Polymers35,2462
Non-polymers5709
Water2,198122
1
A: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0487
Polymers17,6231
Non-polymers4256
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-19 kcal/mol
Surface area8710 Å2
MethodPISA
2
B: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7684
Polymers17,6231
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-26 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.639, 64.288, 80.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11B-352-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 40 or resid 42...
d_2ens_1(chain "B" and (resid 1 through 40 or resid 42...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METTHRA1 - 40
d_12ens_1THRLEUA42 - 49
d_13ens_1ALAILEA51 - 82
d_14ens_1ASNGLUA84 - 131
d_15ens_1CYSVALA133 - 155
d_21ens_1METTHRD1 - 40
d_22ens_1THRLEUD42 - 49
d_23ens_1ALAILED51 - 82
d_24ens_1ASNGLUD84 - 131
d_25ens_1CYSVALD133 - 155

NCS oper: (Code: givenMatrix: (0.0483487524468, -0.998823420156, -0.00376476884243), (-0.998731339825, -0.0482904946908, -0.0142737161844), (0.0140751194678, 0.00445010900043, -0.999891037835)Vector: ...NCS oper: (Code: given
Matrix: (0.0483487524468, -0.998823420156, -0.00376476884243), (-0.998731339825, -0.0482904946908, -0.0142737161844), (0.0140751194678, 0.00445010900043, -0.999891037835)
Vector: 30.9949219361, 32.5904025754, 19.5141882291)

-
Components

#1: Protein Ribonuclease HI / RNase HI / Ribonuclease H / RNase H


Mass: 17622.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rnhA, dasF, herA, rnh, sdrA, b0214, JW0204 / Production host: Escherichia coli (E. coli) / Strain (production host): MIC3001 / References: UniProt: P0A7Y4, ribonuclease H
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30% w/v polyethylene glycol monomethyl ether 5,000

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→48.89 Å / Num. obs: 32256 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 26.51 Å2 / CC1/2: 0.997 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Χ2: 1.03 / Net I/σ(I): 14.9
Reflection shellResolution: 1.76→1.79 Å / Rmerge(I) obs: 0.596 / Num. unique obs: 1799 / CC1/2: 0.913 / Rpim(I) all: 0.381 / Rrim(I) all: 0.706 / Χ2: 0.8

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z0U

4z0u


Resolution: 1.76→48.89 Å / SU ML: 0.216 / Cross valid method: FREE R-VALUE / σ(F): 0.37 / Phase error: 26.2021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2328 2929 4.84 %
Rwork0.2005 57546 -
obs0.202 32256 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.7 Å2
Refinement stepCycle: LAST / Resolution: 1.76→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 31 122 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062608
X-RAY DIFFRACTIONf_angle_d0.80393532
X-RAY DIFFRACTIONf_chiral_restr0.0512364
X-RAY DIFFRACTIONf_plane_restr0.0053456
X-RAY DIFFRACTIONf_dihedral_angle_d20.6958976
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.691980966854 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.790.42571180.32152732X-RAY DIFFRACTION99.75
1.79-1.820.36891530.30782782X-RAY DIFFRACTION99.46
1.82-1.850.30831730.27622691X-RAY DIFFRACTION99.48
1.85-1.890.36321390.25592733X-RAY DIFFRACTION99
1.89-1.930.24081580.25362747X-RAY DIFFRACTION99.11
1.93-1.970.29151480.24252696X-RAY DIFFRACTION98.68
1.97-2.010.29141290.24572774X-RAY DIFFRACTION98.78
2.01-2.060.29091250.23252784X-RAY DIFFRACTION99.42
2.07-2.120.23481140.2312748X-RAY DIFFRACTION98.89
2.12-2.180.25561360.22462745X-RAY DIFFRACTION98.94
2.18-2.250.28831230.22412724X-RAY DIFFRACTION99.06
2.25-2.330.24461490.212776X-RAY DIFFRACTION99.25
2.33-2.430.22381640.21212696X-RAY DIFFRACTION98.93
2.43-2.540.22511520.21582750X-RAY DIFFRACTION99.11
2.54-2.670.23761510.21212743X-RAY DIFFRACTION98.94
2.67-2.840.22211340.22922725X-RAY DIFFRACTION99.2
2.84-3.060.23681260.20842783X-RAY DIFFRACTION98.95
3.06-3.370.25271470.18582715X-RAY DIFFRACTION98.32
3.37-3.850.22981230.16022698X-RAY DIFFRACTION97.18
3.85-4.850.16061470.16042714X-RAY DIFFRACTION98.49
4.85-48.890.21191200.18252790X-RAY DIFFRACTION99.28

+
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