[English] 日本語
Yorodumi
- PDB-7xgt: Crystal structure of rice OsRNase ZS1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xgt
TitleCrystal structure of rice OsRNase ZS1
ComponentsRNase ZS1
KeywordsRNA BINDING PROTEIN / RNase ZS1 / tRNA repair / Zinc
Function / homologyBeta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Os02g0214300 protein
Function and homology information
Biological speciesOryza sativa (Asian cultivated rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMao, Y. / Gao, F. / Chen, Y.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0509903 China
CitationJournal: To Be Published
Title: Crystal structure of rice OsRNase ZS1
Authors: Mao, Y. / Gao, F. / Chen, Y.H.
History
DepositionApr 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNase ZS1
B: RNase ZS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4898
Polymers67,1032
Non-polymers3866
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-173 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.368, 83.148, 87.147
Angle α, β, γ (deg.)90.000, 109.560, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

21A-640-

HOH

31B-571-

HOH

-
Components

#1: Protein RNase ZS1 / Putative nuclear ribonuclease Z


Mass: 33551.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0VGC7
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% PEG 3350, 100 mM Na-citrate pH 5.5, 100 mM KCl

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.7→32.952 Å / Num. obs: 64632 / % possible obs: 98.92 % / Redundancy: 15.2 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.022 / Rrim(I) all: 0.088 / Net I/σ(I): 19.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 15 % / Rmerge(I) obs: 1.38 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6404 / CC1/2: 0.778 / CC star: 0.935 / Rpim(I) all: 0.362 / % possible all: 98.98

-
Processing

Software
NameVersionClassification
PHENIX1.14rc2_3191refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→32.952 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 3175 4.91 %
Rwork0.1723 61457 -
obs0.1736 64632 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.08 Å2 / Biso mean: 38.046 Å2 / Biso min: 13.8 Å2
Refinement stepCycle: final / Resolution: 1.7→32.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4320 0 12 215 4547
Biso mean--60.9 38.15 -
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72490.30831570.2925263098
1.7249-1.75180.31821270.2707263299
1.7518-1.78060.29231470.2556268399
1.7806-1.81130.27311400.2431261698
1.8113-1.84420.2361270.2202267499
1.8442-1.87970.22521380.2068268399
1.8797-1.9180.24011300.1946264899
1.918-1.95970.23631420.1904269799
1.9597-2.00530.21141330.176268199
2.0053-2.05540.2061600.1777261199
2.0554-2.1110.22011580.1816268099
2.111-2.17310.23331410.1745263398
2.1731-2.24320.20131300.1675270199
2.2432-2.32340.21461380.15812670100
2.3234-2.41640.21081170.1723269599
2.4164-2.52630.20081230.1645271099
2.5263-2.65950.18341420.1638265499
2.6595-2.8260.18621360.1701263397
2.826-3.04410.2121360.1737268899
3.0441-3.35010.181350.17392709100
3.3501-3.83430.19841420.1622269299
3.8343-4.82830.16181410.1402269699
4.8283-32.9520.19541350.1719274198

+
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