- PDB-1ssz: Conformational Mapping of Mini-B: An N-terminal/C-terminal Constr... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1ssz
Title
Conformational Mapping of Mini-B: An N-terminal/C-terminal Construct of Surfactant Protein B Using 13C-Enhanced Fourier Transform Infrared (FTIR) Spectroscopy
Components
Pulmonary surfactant-associated protein B
Keywords
SURFACE ACTIVE PROTEIN / LUNG SURFACTANT PROTEIN / SAPOSIN
Function / homology
Function and homology information
Defective pro-SFTPB causes SMDP1 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / Surfactant metabolism ...Defective pro-SFTPB causes SMDP1 and RDS / multivesicular body lumen / lamellar body / alveolar lamellar body / Defective CSF2RB causes SMDP5 / Defective CSF2RA causes SMDP4 / clathrin-coated endocytic vesicle / sphingolipid metabolic process / respiratory gaseous exchange by respiratory system / Surfactant metabolism / multivesicular body / animal organ morphogenesis / lysosome / endoplasmic reticulum membrane / extracellular region Similarity search - Function
Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains ...Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. Similarity search - Domain/homology
EXPERIMENTAL DETAILS. EXPERIMENT TYPE : INFRARED SPECTROSCOPY. TEMPERATURE : 298 PRESSURE : ambient ...EXPERIMENTAL DETAILS. EXPERIMENT TYPE : INFRARED SPECTROSCOPY. TEMPERATURE : 298 PRESSURE : ambient SAMPLE CONTENTS : THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 3,6,7,8,11,13,15,16,18,19,22,25,26,29,30. peptide self-film solvated with hexafluoroispropanol:D20, 9:1 FTIR EXPERIMENTS CONDUCTED : distance geometry; simulated annealing SPECTROMETER MODEL : vector 22 FTIR SPECTROMETER MANUFACTURER : BRUKER STRUCTURE DETERMINATION. SOFTWARE USED : Winfirst, MODELLER 6.3, CHARMM 22 METHOD USED : distance geometry; simulated annealing CONFORMERS, NUMBER CALCULATED : 75 CONFORMERS, NUMBER SUBMITTED : 10 CONFORMERS, SELECTION CRITERIA : structures with acceptable covalent geometry BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM 13-C INDUCED SPECTRAL SHIFTS WHICH GIVE RESIDUE-SPECIFIC SECONDARY STRUCTURE INFORMATION.
Mass: 3934.022 Da / Num. of mol.: 1 / Fragment: residues 208-218, 263-278 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07988
-
Experimental details
-
Experiment
Experiment
Method: INFRARED SPECTROSCOPY
NMR experiment
Type: FTIR
-
Sample preparation
Details
Contents: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES ...Contents: THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 3,6,7,8,11,13,15,16,18,19,22,25,26,29,30. Solvent system: peptide self-film solvated with hexafluoroispropanol:D20, 9:1
Sample conditions
Pressure: ambient / Temperature: 298
-
Data collection
NMR spectrometer
Type: Bruker vector 22 FTIR / Manufacturer: Bruker / Model: vector 22 FTIR
-
Processing
NMR software
Name
Version
Developer
Classification
Winfirst
FTIRcurvefittingsoftware
Kauppineetal.
dataanalysis
MODELLER
6.2
Salietal.
structuresolution
CHARMM
22
Brooksetal.
refinement
Refinement
Method: distance geometry, simulated annealing / Software ordinal: 3 Details: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM 13-C INDUCED SPECTRAL SHIFTS WHICH GIVE RESIDUE-SPECIFIC SECONDARY STRUCTURE INFORMATION.
NMR representative
Selection criteria: fewest violations
NMR ensemble
Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 75 / Conformers submitted total number: 10
+
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.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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