[English] 日本語
Yorodumi
- PDB-9bk1: Crystal structure of Endoribonuclease L-PSP family protein PSPTO0... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bk1
TitleCrystal structure of Endoribonuclease L-PSP family protein PSPTO0102 Sulfur SAD phased
ComponentsL-PSP family protein PSPTO_0102
KeywordsHYDROLASE / Sulfur SAD / Rid protein / Endoribonuclease L-PSP family protein
Function / homologyRutC family, YoaB-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / Endoribonuclease L-PSP family protein
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.57 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Endoribonuclease L-PSP family protein PSPTO0102 Sulfur SAD phased
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-PSP family protein PSPTO_0102


Theoretical massNumber of molelcules
Total (without water)12,8981
Polymers12,8981
Non-polymers00
Water2,594144
1
A: L-PSP family protein PSPTO_0102

A: L-PSP family protein PSPTO_0102

A: L-PSP family protein PSPTO_0102


Theoretical massNumber of molelcules
Total (without water)38,6933
Polymers38,6933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area6260 Å2
ΔGint-26 kcal/mol
Surface area13250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.684, 66.684, 66.684
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

21A-266-

HOH

31A-274-

HOH

41A-328-

HOH

51A-330-

HOH

61A-340-

HOH

71A-344-

HOH

-
Components

#1: Protein L-PSP family protein PSPTO_0102


Mass: 12897.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Gene: PSPTO_0102 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q88BB5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 1.92 Å3/Da / Density % sol: 35.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Magnesium formate dihydrate, 15% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 13020 / % possible obs: 94.1 % / Redundancy: 28.5 % / Biso Wilson estimate: 13.64 Å2 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.005 / Rrim(I) all: 0.029 / Χ2: 1.11 / Net I/σ(I): 118.35
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.073 / Mean I/σ(I) obs: 7.45 / Num. unique obs: 153 / CC1/2: 0.984 / Rpim(I) all: 0.066 / Rrim(I) all: 0.099 / Χ2: 0.848

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data scaling
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.57→47.15 Å / SU ML: 0.1426 / Cross valid method: FREE R-VALUE / σ(F): 0.4 / Phase error: 20.533
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2054 1302 10 %
Rwork0.1772 11718 -
obs0.18 13020 93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.34 Å2
Refinement stepCycle: LAST / Resolution: 1.57→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 0 144 1038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053906
X-RAY DIFFRACTIONf_angle_d0.70741231
X-RAY DIFFRACTIONf_chiral_restr0.0556149
X-RAY DIFFRACTIONf_plane_restr0.0051158
X-RAY DIFFRACTIONf_dihedral_angle_d12.9568335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.640.2204790.1795716X-RAY DIFFRACTION51.56
1.64-1.710.21361470.18051300X-RAY DIFFRACTION95.07
1.71-1.80.23851450.19491360X-RAY DIFFRACTION98.11
1.8-1.910.26441510.19721366X-RAY DIFFRACTION98.19
1.91-2.060.20711500.18251351X-RAY DIFFRACTION98.49
2.06-2.270.21231600.18451393X-RAY DIFFRACTION98.98
2.27-2.60.19811480.17931376X-RAY DIFFRACTION98.07
2.6-3.270.20361570.17731384X-RAY DIFFRACTION98.47
3.28-47.150.18441650.16221472X-RAY DIFFRACTION99.51

+
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