[English] 日本語
Yorodumi
- PDB-7vsd: E. coli Ribonuclease HI in complex with one Mg2+ (2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vsd
TitleE. coli Ribonuclease HI in complex with one Mg2+ (2)
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 / Ribonuclease H domain / RNase H type-1 domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)35,5117
Polymers35,2462
Non-polymers2655
Water2,774154
1
A: 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 area210 Å2
ΔGint-15 kcal/mol
Surface area8680 Å2
MethodPISA
2
B: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7433
Polymers17,6231
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-24 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.363, 85.363, 77.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 27 or resid 30...
d_2ens_1(chain "B" and (resid 1 through 27 or resid 30...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METARGA1 - 27
d_12ens_1GLYGLYA32
d_13ens_1GLULEUA34 - 61
d_14ens_1GLUTHRA63 - 81
d_15ens_1ILELYSA84 - 88
d_16ens_1ARGGLNA90 - 107
d_17ens_1LEUTYRA111 - 155
d_21ens_1METARGB1 - 27
d_22ens_1GLYGLYB32
d_23ens_1GLULEUB34 - 61
d_24ens_1GLUTHRB63 - 81
d_25ens_1ILELYSB84 - 88
d_26ens_1ARGGLNB90 - 107
d_27ens_1LEUTYRB109 - 153

NCS oper: (Code: givenMatrix: (0.998624872191, -0.0523315849907, -0.00312567641369), (-0.0523508562874, -0.998607990582, -0.00643964215359), (-0.00278432876202, 0.00659441865932, -0.99997438025) ...NCS oper: (Code: given
Matrix: (0.998624872191, -0.0523315849907, -0.00312567641369), (-0.0523508562874, -0.998607990582, -0.00643964215359), (-0.00278432876202, 0.00659441865932, -0.99997438025)
Vector: -2.79071565112, 5.14075265612, 19.4272477763)

-
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, 30% w/v polyethylene glycol 4,000

-
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: Apr 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→47.69 Å / Num. obs: 32240 / % possible obs: 99.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 20.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.056 / Rrim(I) all: 0.14 / Net I/σ(I): 10.4
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.95 / Num. unique obs: 1677 / CC1/2: 0.934 / Rpim(I) all: 0.442 / Rrim(I) all: 1.049

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z0u

4z0u


Resolution: 1.7→47.69 Å / SU ML: 0.1724 / Cross valid method: FREE R-VALUE / σ(F): 0.34 / Phase error: 25.3894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.23 2991 4.97 %
Rwork0.1857 57197 -
obs0.1879 32240 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 13 154 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01582570
X-RAY DIFFRACTIONf_angle_d1.51343481
X-RAY DIFFRACTIONf_chiral_restr0.0946361
X-RAY DIFFRACTIONf_plane_restr0.0092449
X-RAY DIFFRACTIONf_dihedral_angle_d22.3853954
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.7429485658 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.30431480.25252699X-RAY DIFFRACTION99.65
1.73-1.760.26231590.24812679X-RAY DIFFRACTION99.2
1.76-1.790.2441260.22952755X-RAY DIFFRACTION99.79
1.79-1.820.27671640.21312745X-RAY DIFFRACTION99.86
1.82-1.860.25031230.21812746X-RAY DIFFRACTION99.76
1.86-1.90.23021490.20412693X-RAY DIFFRACTION99.2
1.9-1.950.27761470.20152727X-RAY DIFFRACTION99.62
1.95-1.990.26671400.19672703X-RAY DIFFRACTION99.09
1.99-2.050.27051110.19742744X-RAY DIFFRACTION99.37
2.05-2.110.21861530.17982715X-RAY DIFFRACTION99.62
2.11-2.180.22161310.17412742X-RAY DIFFRACTION99.72
2.18-2.250.21861440.18592696X-RAY DIFFRACTION99.4
2.25-2.340.22221500.1742748X-RAY DIFFRACTION99.83
2.35-2.450.25051450.19752720X-RAY DIFFRACTION99.93
2.45-2.580.28771590.19442715X-RAY DIFFRACTION99.9
2.58-2.740.21231550.20312714X-RAY DIFFRACTION99.93
2.74-2.950.29951360.18122740X-RAY DIFFRACTION99.76
2.95-3.250.24091290.18452736X-RAY DIFFRACTION99.86
3.25-3.720.22831330.16462746X-RAY DIFFRACTION99.72
3.72-4.690.16741400.16182726X-RAY DIFFRACTION99.51
4.69-47.690.2061490.18732708X-RAY DIFFRACTION99.17

+
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