[English] 日本語
Yorodumi
- PDB-3s6s: Ancylostoma-secreted protein Ac-ASP-7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s6s
TitleAncylostoma-secreted protein Ac-ASP-7
ComponentsAc-ASP-7
KeywordsUNKNOWN FUNCTION / Pathogenesis-related Protein / SCP/TAPS
Function / homologyPathogenesis-related Protein p14a / CAP / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesAncylostoma caninum (dog hookworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.4 Å
AuthorsOsman, A. / Wang, C.K. / Winter, A. / Loukas, A. / Tribolet, L. / Gasser, R. / Hofmann, A.
CitationJournal: Biotechnol Adv
Title: Hookworm SCP/TAPS protein structure--A key to understanding host-parasite interactions and developing new interventions.
Authors: Osman, A. / Wang, C.K. / Winter, A. / Loukas, A. / Tribolet, L. / Gasser, R.B. / Hofmann, A.
History
DepositionMay 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ac-ASP-7
B: Ac-ASP-7


Theoretical massNumber of molelcules
Total (without water)47,0232
Polymers47,0232
Non-polymers00
Water1,802100
1
A: Ac-ASP-7


Theoretical massNumber of molelcules
Total (without water)23,5111
Polymers23,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ac-ASP-7


Theoretical massNumber of molelcules
Total (without water)23,5111
Polymers23,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.352, 79.153, 94.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ac-ASP-7


Mass: 23511.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma caninum (dog hookworm) / Production host: Pichia Pastoris (fungus)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAS PER THE THE AUTHORS THERE IS AN UNEXPLAINED SEQUENCE MISMATCH BETWEEN THE GENBANK SEQUENCE AND ...AS PER THE THE AUTHORS THERE IS AN UNEXPLAINED SEQUENCE MISMATCH BETWEEN THE GENBANK SEQUENCE AND THE SEQUENCE IN THIS STRUCTURE. THE DNA SEQUENCING DATA IS UNAMBIGUOUS AND THE ELECTRON DENSITY CLEARLY SUPPORTS THE AUTHORS ASSIGNMENT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% MPD, 0.1 M TRIS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.93224 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93224 Å / Relative weight: 1
ReflectionResolution: 2.4→61 Å / Num. obs: 18132 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 44.5 Å2 / Rsym value: 0.074
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 2591 / Rsym value: 0.26 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→60 Å / SU ML: 0.34 / σ(F): 1.46 / Phase error: 24.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 921 5.08 %random
Rwork0.1964 ---
obs0.1988 18085 99.98 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.188 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.6512 Å20 Å2-0 Å2
2---0.0045 Å20 Å2
3----5.6466 Å2
Refinement stepCycle: LAST / Resolution: 2.4→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 0 100 2783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082759
X-RAY DIFFRACTIONf_angle_d1.2163704
X-RAY DIFFRACTIONf_dihedral_angle_d16.5491002
X-RAY DIFFRACTIONf_chiral_restr0.092374
X-RAY DIFFRACTIONf_plane_restr0.004493
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47060.31891380.23112690X-RAY DIFFRACTION100
2.4706-2.55030.37151260.24622698X-RAY DIFFRACTION100
2.5503-2.64140.28611750.23762641X-RAY DIFFRACTION100
2.6414-2.7470.29811570.23432624X-RAY DIFFRACTION100
2.747-2.87180.23471440.19312677X-RAY DIFFRACTION100
2.8718-3.0230.26221580.20222645X-RAY DIFFRACTION100
3.023-3.2120.261560.20922652X-RAY DIFFRACTION100
3.212-3.45940.25211120.19562713X-RAY DIFFRACTION100
3.4594-3.80640.24631460.18612686X-RAY DIFFRACTION100
3.8064-4.35460.22591390.17452645X-RAY DIFFRACTION100
4.3546-5.47650.19881500.16322673X-RAY DIFFRACTION100
5.4765-24.71410.18411130.20822696X-RAY DIFFRACTION100

+
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