[English] 日本語
Yorodumi
- PDB-3bqq: Crystal Structure of Human Saposin D (triclinic) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bqq
TitleCrystal Structure of Human Saposin D (triclinic)
ComponentsPROACTIVATOR POLYPEPTIDE
KeywordsLIPID BINDING PROTEIN / SAPOSIN / SPHINGOLIPID ACTIVATOR PROTEIN / ACID CERAMIDASE / FARBER DISEASE / LIPID METABOLISM / LYSOSOME / SPHINGOLIPID METABOLISM
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 / epithelial cell differentiation involved in prostate gland development / Glycosphingolipid catabolism ...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 / epithelial cell differentiation involved in prostate gland development / Glycosphingolipid catabolism / prostate gland growth / lysosomal transport / azurophil granule membrane / regulation of lipid metabolic process / lysosomal lumen / Peptide ligand-binding receptors / enzyme activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / phospholipid binding / late endosome / Platelet degranulation / : / protease binding / scaffold protein binding / G alpha (i) signalling events / lysosome / regulation of autophagy / 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-like / NK-Lysin / 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, chordata / Saposin-like / NK-Lysin / 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. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPrive, G.G. / Popovic, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of the human ceramide activator protein saposin D.
Authors: Popovic, K. / Prive, G.G.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: PROACTIVATOR POLYPEPTIDE
A: PROACTIVATOR POLYPEPTIDE
B: PROACTIVATOR POLYPEPTIDE
D: PROACTIVATOR POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)35,7054
Polymers35,7054
Non-polymers00
Water5,657314
1
A: PROACTIVATOR POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)8,9261
Polymers8,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROACTIVATOR POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)8,9261
Polymers8,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROACTIVATOR POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)8,9261
Polymers8,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PROACTIVATOR POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)8,9261
Polymers8,9261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.660, 41.120, 65.450
Angle α, β, γ (deg.)89.90, 81.20, 71.40
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
PROACTIVATOR POLYPEPTIDE / CERAMIDE ACTIVATOR PROTEIN /


Mass: 8926.332 Da / Num. of mol.: 4 / Fragment: SAPOSIN D, RESIDUES 405-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSAP / Plasmid: PET-16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) ROSETTA-GAMI 2 / References: UniProt: P07602
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4K, ZINC SULFATE, SODIUM ACETATE BUFFER, PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Mar 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→65 Å / Num. obs: 24429 / % possible obs: 92.6 % / Redundancy: 3.52 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.1406 / Mean I/σ(I) obs: 6.73 / % possible all: 91.2

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
PROTEUM PLUSPLUSdata collection
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAPOSIN D P212121

Resolution: 2→64.55 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.71 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24217 1308 5.1 %RANDOM
Rwork0.19514 ---
obs0.19756 24429 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.496 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.25 Å2-0.01 Å2
2---0.04 Å2-0.54 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 0 314 2791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222543
X-RAY DIFFRACTIONr_angle_refined_deg1.3992.0063460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.34526.514109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36215456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.874155
X-RAY DIFFRACTIONr_chiral_restr0.10.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021905
X-RAY DIFFRACTIONr_nbd_refined0.2160.21257
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.210
X-RAY DIFFRACTIONr_mcbond_it0.8451.51686
X-RAY DIFFRACTIONr_mcangle_it1.37522594
X-RAY DIFFRACTIONr_scbond_it1.88531000
X-RAY DIFFRACTIONr_scangle_it3.0144.5856
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 107 -
Rwork0.224 1736 -
obs--91.19 %

+
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