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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yag
TitleCrystal structure of PnrA from S. pneumoniae in complex with thymidine
ComponentsLipoprotein
KeywordsTRANSPORT PROTEIN / Nucleoside substrate-binding protein
Function / homologyABC 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 / ACETATE ION / NICKEL (II) ION / THYMIDINE / Lipoprotein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 12, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
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)141,43316
Polymers139,9944
Non-polymers1,43912
Water4,576254
1
C: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2993
Polymers34,9981
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2993
Polymers34,9981
Non-polymers3012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3584
Polymers34,9981
Non-polymers3603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4766
Polymers34,9981
Non-polymers4775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.966, 303.818, 128.417
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-505-

HOH

21B-560-

HOH

31B-572-

HOH

41B-573-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12C
22B
13C
23D
14A
24B
15A
25D
16B
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROCA4 - 3312 - 329
21SERSERPROPROAB4 - 3312 - 329
12SERSERPROPROCA4 - 3312 - 329
22SERSERPROPROBC4 - 3312 - 329
13HISHISPROPROCA5 - 3313 - 329
23HISHISPROPRODD5 - 3313 - 329
14SERSERGLUGLUAB4 - 3322 - 330
24SERSERGLUGLUBC4 - 3322 - 330
15HISHISPROPROAB5 - 3313 - 329
25HISHISPROPRODD5 - 3313 - 329
16HISHISPROPROBC5 - 3313 - 329
26HISHISPROPRODD5 - 3313 - 329

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Lipoprotein /


Mass: 34998.469 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-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-THM / THYMIDINE / DEOXYTHYMIDINE / 2'-DEOXYTHYMIDINE / Thymidine


Type: DNA OH 5 prime terminus / Mass: 242.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
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: 0.979336 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979336 Å / Relative weight: 1
ReflectionResolution: 2.55→49.21 Å / Num. obs: 50223 / % possible obs: 99.2 % / Redundancy: 7.2 % / CC1/2: 0.96 / Rpim(I) all: 0.16 / Net I/σ(I): 5.1
Reflection shellResolution: 2.55→2.63 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4624 / CC1/2: 0.52 / Rpim(I) all: 0.71

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FQW

2fqw


Resolution: 2.55→49.21 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.4 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.667 / ESU R Free: 0.308
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 2579 5.1 %RANDOM
Rwork0.2085 ---
obs0.2108 47620 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.13 Å2 / Biso mean: 47.42 Å2 / Biso min: 11.41 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å20 Å2
2---0.28 Å20 Å2
3----1.96 Å2
Refinement stepCycle: final / Resolution: 2.55→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9852 0 79 254 10185
Biso mean--37.26 35.23 -
Num. residues----1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310125
X-RAY DIFFRACTIONr_bond_other_d0.0020.0189103
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.62713689
X-RAY DIFFRACTIONr_angle_other_deg1.2631.58721208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83951324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26625.537484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.242151646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3371518
X-RAY DIFFRACTIONr_chiral_restr0.0610.21306
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021992
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C99760.08
12A99760.08
21C99560.08
22B99560.08
31C99770.08
32D99770.08
41A99950.07
42B99950.07
51A99370.07
52D99370.07
61B100300.06
62D100300.06
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 191 -
Rwork0.316 3503 -
all-3694 -
obs--99.68 %

+
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