[English] 日本語
Yorodumi
- PDB-1nnt: STRUCTURAL EVIDENCE FOR A PH-SENSITIVE DI-LYSINE TRIGGER IN THE H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nnt
TitleSTRUCTURAL EVIDENCE FOR A PH-SENSITIVE DI-LYSINE TRIGGER IN THE HEN OVOTRANSFERRIN N-LOBE: IMPLICATIONS FOR TRANSFERRIN IRON RELEASE
ComponentsOVOTRANSFERRIN
KeywordsIRON TRANSPORT PROTEIN
Function / homology
Function and homology information


extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / iron ion transport / antibacterial humoral response / response to lipopolysaccharide ...extracellular sequestering of iron ion / organomineral extracellular matrix / antimicrobial humoral response / intracellular sequestering of iron ion / ferric iron binding / acute-phase response / recycling endosome / iron ion transport / antibacterial humoral response / response to lipopolysaccharide / early endosome / response to xenobiotic stimulus / iron ion binding / extracellular space / plasma membrane
Similarity search - Function
Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II ...Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin-like domain / Transferrin / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Ovotransferrin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsDewan, J.C. / Mikami, B. / Sacchettini, J.C.
CitationJournal: Biochemistry / Year: 1993
Title: Structural evidence for a pH-sensitive dilysine trigger in the hen ovotransferrin N-lobe: implications for transferrin iron release.
Authors: Dewan, J.C. / Mikami, B. / Hirose, M. / Sacchettini, J.C.
History
DepositionSep 15, 1993Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Remark 650HELIX HELIX NAMES ARE SIMILAR TO HUMAN LACTOFERRIN (TABLE 3, J. MOL. BIOL., VOL. 209, P. 711, 1993) ...HELIX HELIX NAMES ARE SIMILAR TO HUMAN LACTOFERRIN (TABLE 3, J. MOL. BIOL., VOL. 209, P. 711, 1993) WHICH ARE SIMILAR TO THE RABBIT SERUM TRANSFERRIN STRUCTURE (BIOCHEMISTRY, VOL. 27, P. 5804, 1988). HELIX NAMES FOR RESIDUES 167 - 174 ARE NOT NOTED IN LACTOFERRIN STRUCTURE.
Remark 700SHEET IN SHEET RECORDS BELOW, STRAND NAMES ARE SAME AS HUMAN LACTOFERRIN (TABLE 3, J. MOL. BIOL., ...SHEET IN SHEET RECORDS BELOW, STRAND NAMES ARE SAME AS HUMAN LACTOFERRIN (TABLE 3, J. MOL. BIOL., VOL. 209, P. 711, 1993) WHICH ARE SAME AS THE RABBIT SERUM TRANSFERRIN STRUCTURE (BIOCHEMISTRY, VOL. 27, P. 5804, 1988).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OVOTRANSFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2223
Polymers36,1061
Non-polymers1162
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.940, 91.790, 75.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 71 / 2: CIS PROLINE - PRO 287
3: THERE IS A STRONG 2.3 ANGSTROMS H-BOND BETWEEN NZ OF LYS 209 AND NZ OF LYS 301 WHICH IT IS SUGGESTED FORMS A PH-SENSITIVE DI-LYSINE TRIGGER THAT OPENS THE TWO DOMAINS OF THE N-LOBE AT LOW PH AND ...3: THERE IS A STRONG 2.3 ANGSTROMS H-BOND BETWEEN NZ OF LYS 209 AND NZ OF LYS 301 WHICH IT IS SUGGESTED FORMS A PH-SENSITIVE DI-LYSINE TRIGGER THAT OPENS THE TWO DOMAINS OF THE N-LOBE AT LOW PH AND FACILITATES FE(III) RELEASE.

-
Components

#1: Protein OVOTRANSFERRIN


Mass: 36105.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P02789
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHERE IS A STRONG 2.3 ANGSTROMS H-BOND BETWEEN NZ OF LYS 209 AND NZ OF LYS 301 WHICH IT IS ...THERE IS A STRONG 2.3 ANGSTROMS H-BOND BETWEEN NZ OF LYS 209 AND NZ OF LYS 301 WHICH IT IS SUGGESTED FORMS A PH-SENSITIVE DI-LYSINE TRIGGER THAT OPENS THE TWO DOMAINS OF THE N-LOBE AT LOW PH AND FACILITATES FE(III) RELEASE.
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TRFE_CHICK SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE VAL 64 ALA 64 ILE 81 VAL 81 TRP 135 ARG 135 LEU 220 GLN 220 ASN 221 LYS 221 THE FOLLOWING RESIDUES ARE MISSING FROM THE N-TERMINUS SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY ALA 1 PRO 2 PRO 3 LYS 4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal grow
*PLUS
pH: 5.9 / Method: vapor diffusion, hanging drop / Details: used to seed
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
159 mg/mlprotein1drop
20.02 Macetate1drop
30.01 %1dropNaN3
44-5 %PEG60001drop
50.02 Macetate1drop
64-5 %PEG60001reservoir
70.02 Macetate1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 14266 / % possible obs: 94 % / Observed criterion σ(I): 8.6 / Num. measured all: 59108 / Rmerge(I) obs: 0.09

-
Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.16 / Rfactor obs: 0.16 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 5 108 2646
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 8965 / σ(I): 2 / Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.25

+
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://pdbjlvh1.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