[English] 日本語
Yorodumi
- PDB-6slr: Structure of saposin B in complex with atovaquone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6slr
TitleStructure of saposin B in complex with atovaquone
ComponentsProsaposin
KeywordsLIPID BINDING PROTEIN / glycoprotein / lysosome / protein-ligand complex / atovaquone
Function / homology
Function and homology information


positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development ...positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development / Glycosphingolipid catabolism / lysosomal transport / azurophil granule membrane / regulation of lipid metabolic process / enzyme activator activity / lysosomal lumen / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Peptide ligand-binding receptors / regulation of autophagy / phospholipid binding / late endosome / Platelet degranulation / G alpha (i) signalling events / scaffold protein binding / protease binding / collagen-containing extracellular matrix / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Saposin, chordata / 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, chordata / 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
Chem-AOQ / Prosaposin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsZubieta, C. / Milliken, B. / Doyle, R.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyATIP-Avenir France
CitationJournal: To Be Published
Title: Structure of saposin B in complex with atovaquone
Authors: Zubieta, C. / Milliken, B. / Doyle, R.
History
DepositionAug 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prosaposin
B: Prosaposin
C: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9158
Polymers26,9053
Non-polymers1,0105
Water1,04558
1
A: Prosaposin
C: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3964
Polymers17,9372
Non-polymers4592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prosaposin
hetero molecules

B: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0398
Polymers17,9372
Non-polymers1,1026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Unit cell
Length a, b, c (Å)75.707, 75.707, 95.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-203-

AOQ

21B-203-

AOQ

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERCYSCYSAA0 - 773 - 80
21SERSERCYSCYSBB0 - 773 - 80
12SERSERCYSCYSAA0 - 773 - 80
22SERSERCYSCYSCC0 - 773 - 80
13GLYGLYASPASPBB-2 - 781 - 81
23GLYGLYASPASPCC-2 - 781 - 81

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Prosaposin / Proactivator polypeptide


Mass: 8968.339 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSAP, GLBA, SAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07602
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-AOQ / 2-[trans-4-(4-chlorophenyl)cyclohexyl]-3-hydroxynaphthalene-1,4-dione / Atovaquone


Mass: 366.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19ClO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, Antimicrobial*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES, 30% PEG6000 / PH range: 5-6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.91→38.62 Å / Num. obs: 14331 / % possible obs: 91.8 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Net I/σ(I): 15.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.927-2.182.40.4167180.8250.3120.52371.1
6.455-38.65.60.0287170.9990.0130.03198.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4V2O

4v2o


Resolution: 2.38→38.62 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 20.247 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 715 5.5 %RANDOM
Rwork0.2326 ---
obs0.2349 12391 99.46 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 138.3 Å2 / Biso mean: 76.973 Å2 / Biso min: 40.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: final / Resolution: 2.38→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 96 58 1989
Biso mean--88.8 71.31 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131974
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181771
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.72669
X-RAY DIFFRACTIONr_angle_other_deg1.271.6194143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9645240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32225.33390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.571156
X-RAY DIFFRACTIONr_chiral_restr0.0660.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02353
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A22290.1
12B22290.1
21A22170.1
22C22170.1
31B23020.11
32C23020.11
LS refinement shellResolution: 2.38→2.44 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.308 50 -
Rwork0.322 898 -
obs--97.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.67110.2762-0.05412.8979-0.92424.60.01170.491-0.4316-0.0980.07960.13610.4768-0.3809-0.09130.1432-0.0774-0.00080.1697-0.07290.084342.456-19.12816.972
25.268-0.0379-2.19953.16541.62746.1498-0.0065-0.5543-0.29640.37980.1368-0.56240.49271.339-0.13030.1180.033-0.08360.39740.03640.124334.59760.89920.023
33.5512-0.00240.3652.8574-1.34915.7790.0616-0.4422-0.39370.13070.26050.39860.4873-0.921-0.32210.2626-0.01770.07590.22940.11680.129733.442-17.41525.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 78
2X-RAY DIFFRACTION2B-2 - 78
3X-RAY DIFFRACTION3C-2 - 78

+
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