[English] 日本語
Yorodumi
- PDB-2moq: Solution Structure and Molecular determinants of Hemoglobin Bindi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2moq
TitleSolution Structure and Molecular determinants of Hemoglobin Binding of the first NEAT Domain of IsdB in Staphylococcus aureus
ComponentsIron-regulated surface determinant protein B
KeywordsPROTEIN BINDING / Neat domain / IsdB / Hemoglobin receptor / Staphylococcus aureus / Iron surface determinant protein / METAL BINDING PROTEIN
Function / homology
Function and homology information


heme transmembrane transporter activity / extracellular region / metal ion binding
Similarity search - Function
Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : ...Iron-regulated surface determinant protein IsdB / : / Iron-regulated surface determinant protein H/B, linker domain / Immunoglobulin-like - #1850 / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / : / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Iron-regulated surface determinant protein B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, molecular dynamics
Model detailslowest energy, model1
AuthorsFonner, B.A. / Tripet, B.P. / Eilers, B.J. / Stanisich, J. / Sullivan-Springhetti, R.K. / Moore, R. / Lui, M. / Lei, B. / Copie, V.
Citation
Journal: Biochemistry / Year: 2014
Title: Solution Structure and Molecular Determinants of Hemoglobin Binding of the First NEAT Domain of IsdB in Staphylococcus aureus.
Authors: Fonner, B.A. / Tripet, B.P. / Eilers, B.J. / Stanisich, J. / Sullivan-Springhetti, R.K. / Moore, R. / Liu, M. / Lei, B. / Copie, V.
#1: Journal: Biomol.Nmr Assign. / Year: 2014
Title: 1H, 13C, 15N backbone and side chain NMR resonance assignments of the N-terminal NEAr iron transporter domain 1 (NEAT 1) of the hemoglobin receptor IsdB of Staphylococcus aureus.
Authors: Fonner, B.A. / Tripet, B.P. / Lui, M. / Zhu, H. / Lei, B. / Copie, V.
History
DepositionApr 29, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Iron-regulated surface determinant protein B


Theoretical massNumber of molelcules
Total (without water)19,1091
Polymers19,1091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein Iron-regulated surface determinant protein B / Fur-regulated protein B / Staphylococcal iron-regulated protein H / Staphylococcus aureus surface protein J


Mass: 19109.414 Da / Num. of mol.: 1 / Fragment: NEAT 1 domain, UNP residues 125-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MW2 / Gene: isdB, frpB, sasJ, sirH, MW1011 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NX66

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N TOCSY
1313D 1H-15N NOESY
1423D CBCA(CO)NH
1523D C(CO)NH
1623D HNCA
1723D HN(CA)CB
1823D HBHA(CO)NH
1923D H(CCO)NH
11033D (H)CCH-TOCSY
11133D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 15N] IsdB N1, 50 mM sodium phosphate, 400 mM sodium chloride, 0.1 mM PMSF, 1 mM EDTA, 0.01 % sodium azide, 5 % [U-99% 2H] D2O, 95 % H2O, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-99% 13C; U-99% 15N] IsdB N1, 50 mM sodium phosphate, 400 mM sodium chloride, 0.1 mM PMSF, 1 mM EDTA, 0.01 % sodium azide, 5 % [U-99% 2H] D2O, 95 % H2O, 95% H2O/5% D2O95% H2O/5% D2O
31 mM [U-99% 13C; U-99% 15N] IsdB N1, 50 mM sodium phosphate, 400 mM sodium chloride, 0.1 mM PMSF, 1 mM EDTA, 0.01 % sodium azide, 100 % [U-99% 2H] D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMIsdB N1-1[U-99% 15N]1
50 mMsodium phosphate-21
400 mMsodium chloride-31
0.1 mMPMSF-41
1 mMEDTA-51
0.01 %sodium azide-61
5 %D2O-7[U-99% 2H]1
95 %H2O-81
1 mMIsdB N1-9[U-99% 13C; U-99% 15N]2
50 mMsodium phosphate-102
400 mMsodium chloride-112
0.1 mMPMSF-122
1 mMEDTA-132
0.01 %sodium azide-142
5 %D2O-15[U-99% 2H]2
95 %H2O-162
1 mMIsdB N1-17[U-99% 13C; U-99% 15N]3
50 mMsodium phosphate-183
400 mMsodium chloride-193
0.1 mMPMSF-203
1 mMEDTA-213
0.01 %sodium azide-223
100 %D2O-23[U-99% 2H]3
Sample conditionsIonic strength: 0.45 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
NMRPipe7.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDraw7.4Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
Sparky3.113Goddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: torsion angle dynamics, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / 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