[English] 日本語
Yorodumi
- PDB-3s64: Saposin-like protein Ac-SLP-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s64
TitleSaposin-like protein Ac-SLP-1
ComponentsSaposin-like protein 1
KeywordsLIPID BINDING PROTEIN / Saposin / Lipid-binding
Function / homology
Function and homology information


Saposin-like / NK-Lysin / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Saposin-like protein 1
Similarity search - Component
Biological speciesAncylostoma caninum (dog hookworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.301 Å
AuthorsWillis, C. / Wang, C.K. / Osman, A. / Simon, A. / Mulvenna, J. / Pickering, D. / Riboldi-Tunicliffe, A. / Jones, M.K. / Loukas, A. / Hofmann, A.
CitationJournal: Plos One / Year: 2011
Title: Insights into the membrane interactions of the saposin-like proteins Na-SLP-1 and Ac-SLP-1 from human and dog hookworm.
Authors: Willis, C. / Wang, C.K. / Osman, A. / Simon, A. / Pickering, D. / Mulvenna, J. / Riboldi-Tunicliffe, A. / Jones, M.K. / Loukas, A. / Hofmann, A.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Saposin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9753
Polymers9,5441
Non-polymers4302
Water57632
1
A: Saposin-like protein 1
hetero molecules

A: Saposin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9496
Polymers19,0892
Non-polymers8614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/31
Buried area1610 Å2
ΔGint-16 kcal/mol
Surface area8470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.053, 72.053, 90.888
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein Saposin-like protein 1 / Ac-SLP-1


Mass: 9544.258 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 18-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ancylostoma caninum (dog hookworm) / Gene: SLP1 / Production host: Pichia pastoris (fungus) / References: UniProt: Q0MRQ4
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 1.35M sodium citrate, 0.1M HEPES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9536 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.2→37 Å / Num. obs: 6649 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 49 Å2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 14.9 % / Rsym value: 0.461 / % 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: SIRAS / Resolution: 2.301→23.585 Å / SU ML: 0.31 / σ(F): 1.45 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 535 4.57 %RANDOM
Rwork0.2249 ---
obs0.2261 6313 99.87 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.5 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.2479 Å2-0 Å2-0 Å2
2--7.2479 Å20 Å2
3----14.4957 Å2
Refinement stepCycle: LAST / Resolution: 2.301→23.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms606 0 28 32 666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008643
X-RAY DIFFRACTIONf_angle_d1.183866
X-RAY DIFFRACTIONf_dihedral_angle_d20.618258
X-RAY DIFFRACTIONf_chiral_restr0.078102
X-RAY DIFFRACTIONf_plane_restr0.004107
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3014-2.53280.34021450.27092778
2.5328-2.89870.32161270.25442814
2.8987-3.64990.28781150.22392791
3.6499-23.58620.20791480.20652791

+
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