[English] 日本語
Yorodumi
- PDB-1pxu: Crystal structure of chicken NtA from a eukaryotic source at 2.2A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pxu
TitleCrystal structure of chicken NtA from a eukaryotic source at 2.2A resolution
Componentsagrin
KeywordsSTRUCTURAL PROTEIN / Agrin
Function / homology
Function and homology information


extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / dystroglycan binding / basal part of cell ...extracellular matrix of synaptic cleft / acetylcholine receptor regulator activity / positive regulation of synaptic assembly at neuromuscular junction / skeletal muscle acetylcholine-gated channel clustering / chondroitin sulfate binding / laminin-1 binding / sialic acid binding / neuron cell-cell adhesion / dystroglycan binding / basal part of cell / photoreceptor ribbon synapse / filopodium assembly / glycosaminoglycan binding / heparan sulfate proteoglycan binding / extracellular matrix binding / positive regulation of filopodium assembly / neuromuscular junction development / transmembrane receptor protein tyrosine kinase activator activity / receptor clustering / basement membrane / laminin binding / extracellular matrix / positive regulation of GTPase activity / brain development / neuromuscular junction / negative regulation of neuron projection development / signaling receptor activity / nervous system development / heparin binding / actin cytoskeleton organization / cell differentiation / membrane raft / axon / glutamatergic synapse / synapse / calcium ion binding / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / plasma membrane
Similarity search - Function
NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / Domain found in sea urchin sperm protein, enterokinase, agrin ...NtA (N-terminal agrin) domain / Agrin NtA domain / NtA (N-terminal agrin) domain profile. / Follistatin-like, N-terminal / Follistatin-N-terminal domain-like / Factor I / membrane attack complex / factor I membrane attack complex / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / : / Domain found in sea urchin sperm protein, enterokinase, agrin / Laminin G domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / SEA domain superfamily / Kazal-type serine protease inhibitor domain / Laminin-type EGF domain / Kazal-type serine protease inhibitor domain / SEA domain profile. / SEA domain / SEA domain / Laminin G domain profile. / Kazal type serine protease inhibitors / Laminin G domain / Laminin G domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStetefeld, J.
CitationJournal: Matrix Biol. / Year: 2005
Title: Structure and laminin-binding specificity of the NtA domain expressed in eukaryotic cells.
Authors: Mascarenhas, J.B. / Ruegg, M.A. / Sasaki, T. / Eble, J.A. / Engel, J. / Stetefeld, J.
History
DepositionJul 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: agrin


Theoretical massNumber of molelcules
Total (without water)15,1741
Polymers15,1741
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.685, 50.401, 54.571
Angle α, β, γ (deg.)90.00, 118.93, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein agrin


Mass: 15174.345 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: Q90685, UniProt: P31696*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: peg 8000, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8795 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2002
RadiationMonochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8795 Å / Relative weight: 1
ReflectionResolution: 2.2→28 Å / Num. all: 89789 / Num. obs: 10565 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15.6 Å2 / Rsym value: 0.082

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1jb3

1jb3


Resolution: 2.2→28.03 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 899997.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1081 10.3 %RANDOM
Rwork0.197 ---
obs0.197 10451 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6882 Å2 / ksol: 0.295159 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20 Å2-2.63 Å2
2--1.03 Å20 Å2
3----4.73 Å2
Refine analyzeLuzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 0 75 1137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 176 10.6 %
Rwork0.245 1490 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION5WATER.PARAM

+
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://pdbjlc1.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