[English] 日本語
Yorodumi
- PDB-6ya3: Crystal structure of PnrA from S. pneumoniae in complex with guanosine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ya3
TitleCrystal structure of PnrA from S. pneumoniae in complex with guanosine
ComponentsLipoprotein
KeywordsTRANSPORT PROTEIN / Nucleoside substrate-binding protein
Function / homology: / ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / GUANOSINE / NICKEL (II) ION / Lipoprotein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBatuecas, M.T. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2017-90030-P Spain
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Crystal Structure and Pathophysiological Role of the Pneumococcal Nucleoside-binding Protein PnrA.
Authors: Abdullah, M.R. / Batuecas, M.T. / Jennert, F. / Voss, F. / Westhoff, P. / Kohler, T.P. / Molina, R. / Hirschmann, S. / Lalk, M. / Hermoso, J.A. / Hammerschmidt, S.
History
DepositionMar 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Lipoprotein
A: Lipoprotein
B: Lipoprotein
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,11316
Polymers140,5114
Non-polymers1,60312
Water7,134396
1
C: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5875
Polymers35,1281
Non-polymers4594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5284
Polymers35,1281
Non-polymers4013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5284
Polymers35,1281
Non-polymers4013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4703
Polymers35,1281
Non-polymers3422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.784, 304.919, 128.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-581-

HOH

21B-604-

HOH

31D-531-

HOH

-
Components

#1: Protein
Lipoprotein


Mass: 35127.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: SP_0845 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UPF3
#2: Chemical
ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28% PEG 600, 0.2 M calcium acetate and 0.1 M sodium cacodylate (pH 6.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979264 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979264 Å / Relative weight: 1
ReflectionResolution: 2.28→49.23 Å / Num. obs: 70796 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rpim(I) all: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.28→2.33 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4526 / CC1/2: 0.62 / Rpim(I) all: 0.69

-
Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQW

2fqw


Resolution: 2.28→49.18 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.25 --RANDOM
Rwork0.21 ---
obs-70796 99.7 %-
Displacement parametersBiso max: 161.69 Å2 / Biso mean: 47.8637 Å2 / Biso min: 16.45 Å2
Refinement stepCycle: LAST / Resolution: 2.28→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9906 0 88 398 10392

+
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