[English] 日本語
Yorodumi
- PDB-3zfj: N-terminal domain of pneumococcal PhtD protein with bound Zn(II) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zfj
TitleN-terminal domain of pneumococcal PhtD protein with bound Zn(II)
ComponentsPNEUMOCOCCAL HISTIDINE TRIAD PROTEIN D
KeywordsZINC-BINDING PROTEIN / ZINC TRANSFER
Function / homologyStreptococcal histidine triad repeat / Histidine triad protein / PhtA domain superfamily / Streptococcal histidine triad protein / Pneumococcal histidine triad protein D / Pneumococcal histidine triad protein D
Function and homology information
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodSOLUTION NMR / UNIO10, ARIA
AuthorsBersch, B. / Bougault, C. / Favier, A. / Gabel, F. / Roux, L. / Vernet, T. / Durmort, C.
Citation
Journal: Plos One / Year: 2013
Title: New Insights Into Histidine Triad Proteins: Solution Structure of a Streptococcus Pneumoniae Phtd Domain and Zinc Transfer to Adcaii.
Authors: Bersch, B. / Bougault, C. / Roux, L. / Favier, A. / Vernet, T. / Durmort, C.
#1: Journal: Biochemistry / Year: 2011
Title: Biochemical Characterization of the Histidine Triad Protein Phtd as a Cell Surface Zinc-Binding Protein of Pneumococcus.
Authors: Loisel, E. / Chimalapati, S. / Bougault, C. / Imberty, A. / Gallet, B. / Di Guilmi, A.M. / Brown, J. / Vernet, T. / Durmort, C.
History
DepositionDec 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_exptl_sample_conditions / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PNEUMOCOCCAL HISTIDINE TRIAD PROTEIN D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8482
Polymers15,7821
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000TOTAL ENERGY
RepresentativeModel #1

-
Components

#1: Protein PNEUMOCOCCAL HISTIDINE TRIAD PROTEIN D / PHTD


Mass: 15782.420 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: D39 / Plasmid: PLIM09-T-PHTD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q04KS8, UniProt: A0A0H2ZP82*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Sequence detailsRESIDUES 2-138 OF THE T-PHTD SEQUENCE CORRESPOND TO RESIDUES 30-166 OF THE Q04KS8 ENTRY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-HSQC
12113C-HSQC
1313D-15N- NOESY
1413D-13C-NOESY
2522D- NOESY
NMR detailsText: BACKBONE ASSIGNMENT FROM STANDARD TRIPLE RESONANCE EXPERIMENTS. CCONH-TOCSY AND 3D-NOESY EXPERIMENTS FOR SIDECHAIN ASSIGNMENT. 2 3D-NOESY AND A 2D-NOESY IN D2O FOR THE EXTRACTION OF DISTANCE CONSTRAINTS.

-
Sample preparation

Details
Solution-IDContents
190% WATER, 10% D2O
2100% D2O
Sample conditionsIonic strength: 50 mM / pH: 6.3 / Pressure: 1 atm / Temperature: 308.0 K

-
NMR measurement

NMR spectrometerType: Varian VNMRS800 / Manufacturer: Varian / Model: VNMRS800 / Field strength: 800 MHz

-
Processing

NMR software
NameDeveloperClassification
CNSBRUNGERrefinement
CYANAstructure solution
CNSstructure solution
RefinementMethod: UNIO10, ARIA / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 1000 / Conformers submitted total number: 20

+
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