[English] 日本語
Yorodumi
- PDB-2y7n: Structure of N-terminal domain of Candida albicans als9-2 - Apo Form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y7n
TitleStructure of N-terminal domain of Candida albicans als9-2 - Apo Form
ComponentsAGGLUTININ-LIKE ALS9 PROTEIN
KeywordsCELL ADHESION / ADHESIN / PEPTIDE BINDING PROTEIN
Function / homology
Function and homology information


cell adhesion involved in multi-species biofilm formation / fungal-type cell wall / cell adhesion involved in single-species biofilm formation / side of membrane / cell adhesion molecule binding / cell-cell adhesion / cell adhesion / extracellular region / plasma membrane
Similarity search - Function
Agglutinin-like protein, N-terminal domain, N2 subdomain / Agglutinin-like protein repeat / Agglutinin-like protein, N-terminal / Agglutinin-like protein / Agglutinin-like protein, N-terminal, N2 subdomain / Candida agglutinin-like (ALS) / Agglutinin-like protein, N-terminal domain / Cell-wall agglutinin N-terminal ligand-sugar binding / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 ...Agglutinin-like protein, N-terminal domain, N2 subdomain / Agglutinin-like protein repeat / Agglutinin-like protein, N-terminal / Agglutinin-like protein / Agglutinin-like protein, N-terminal, N2 subdomain / Candida agglutinin-like (ALS) / Agglutinin-like protein, N-terminal domain / Cell-wall agglutinin N-terminal ligand-sugar binding / Immunoglobulin-like - #1280 / Fibrogen-binding domain 1 / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Agglutinin-like protein 9 / :
Similarity search - Component
Biological speciesCANDIDA ALBICANS (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSalgado, P.S. / Cota, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural Basis for the Broad Specificity to Host- Cell Ligands by the Pathogenic Fungus Candida Albicans.
Authors: Salgado, P.S. / Yan, R. / Taylor, J.D. / Burchell, L. / Jones, R. / Hoyer, L.L. / Matthews, S.J. / Simpson, P.J. / Cota, E.
History
DepositionJan 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AGGLUTININ-LIKE ALS9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)33,5741
Polymers33,5741
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.723, 68.717, 120.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein AGGLUTININ-LIKE ALS9 PROTEIN / NT_ALS9-2


Mass: 33573.992 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 18-328
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Plasmid: PET32 XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): ORIGAMI / References: UniProt: Q5A8T1, UniProt: A0A1D8PQ86*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE EXCLUDES N-TERMINAL SIGNAL SEQUENCE (18 RESIDUES)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20201 / % possible obs: 99.7 % / Observed criterion σ(I): 3.4 / Redundancy: 8.5 % / Biso Wilson estimate: 23.243 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.4 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.115 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23638 1034 5.1 %RANDOM
Rwork0.19382 ---
obs0.19593 19118 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.414 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→34.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 0 163 2515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0222412
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.9343306
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9575310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.125.20896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58415351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.027154
X-RAY DIFFRACTIONr_chiral_restr0.1270.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211829
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.998→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 91 -
Rwork0.238 1335 -
obs--96.88 %

+
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