[English] 日本語
Yorodumi
- PDB-2zqb: Crystal structure of a psychrotrophic RNaseHI variant with sextup... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zqb
TitleCrystal structure of a psychrotrophic RNaseHI variant with sextuple thermostabilizing mutations
ComponentsRibonuclease HI
KeywordsHYDROLASE / Cytoplasm / Endonuclease / Magnesium / Metal-binding / Nuclease
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / RNA-DNA hybrid ribonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm
Similarity search - Function
Ribonuclease HI / : / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsAngkawidjaja, C. / Kanaya, S.
CitationJournal: Febs J. / Year: 2009
Title: Destabilization of psychrotrophic RNase HI in a localized fashion as revealed by mutational and X-ray crystallographic analyses
Authors: Rohman, M.S. / Tadokoro, T. / Angkawidjaja, C. / Abe, Y. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S.
History
DepositionAug 7, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 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
C: Ribonuclease HI
D: Ribonuclease HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8497
Polymers70,5614
Non-polymers2883
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.239, 68.239, 272.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein
Ribonuclease HI / RNase HI


Mass: 17640.176 Da / Num. of mol.: 4 / Mutation: N29K, D39G, M76V, K90N, R97G, D136H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Plasmid: pET25b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): MIC2067(DE3) / References: UniProt: Q8EE30, ribonuclease H
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG, MME 5000, 0.1M MES, 0.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 2, 2008 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 23782 / % possible obs: 100 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 28.4
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 6.39 / Num. unique all: 2299 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E4L

2e4l


Resolution: 2.49→47.51 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.093 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.684 / ESU R Free: 0.295
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1212 5.1 %RANDOM
Rwork0.19312 ---
obs0.19583 22450 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.584 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.49→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4702 0 15 224 4941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0214851
X-RAY DIFFRACTIONr_angle_refined_deg2.511.9346566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5415594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25424.115209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45615843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4431524
X-RAY DIFFRACTIONr_chiral_restr0.1780.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023638
X-RAY DIFFRACTIONr_nbd_refined0.2650.22363
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23137
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4070.26
X-RAY DIFFRACTIONr_mcbond_it1.6011.53105
X-RAY DIFFRACTIONr_mcangle_it2.53324734
X-RAY DIFFRACTIONr_scbond_it3.55132149
X-RAY DIFFRACTIONr_scangle_it5.3544.51832
LS refinement shellResolution: 2.487→2.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 88 -
Rwork0.221 1571 -
obs--96.79 %

+
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